Immunomodulatory proteins with tunable affinities

ABSTRACT

Provided are immunomodulatory proteins and nucleic acids encoding such proteins. The immunomodulatory proteins provide therapeutic utility for a variety of immunological and oncological conditions. Compositions and methods for making and using such proteins are provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority from U.S. provisional application No. 62/149,437 filed Apr. 17, 2015, entitled “Immunomodulatory Proteins with Tunable Affinities” and to U.S. provisional application No. 62/218,534 filed Sep. 14, 2015, entitled “Immunomodulatory Proteins with Tunable Affinities,” the contents of each of which are incorporated by reference in their entirety.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING

The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled 761612000140SEQLIST.TXT, created Apr. 15, 2016, which is 377 kilobytes in size. The information in the electronic format of the Sequence Listing is incorporated by reference in its entirety.

FIELD

The present invention relates to therapeutic proteins for modulating immune response in the treatment of cancer and immunological diseases.

BACKGROUND

Modulation of the immune response by intervening in the processes that occur in the immunological synapse (IS) formed by and between antigen-presenting cells (APCs) or target cells and lymphocytes is of increasing medical interest. Currently, biologics used to enhance or suppress immune response have generally been limited to immunoglobulins (e.g., anti-PD-1 mAbs) or soluble receptors (e.g., Fc-CTLA4). Soluble receptors suffer from a number of deficiencies. While useful for antagonizing interactions between proteins, soluble receptors often lack the ability to agonize such interactions. Antibodies have proven less limited in this regard and examples of both agonistic and antagonistic antibodies are known in the art. Nevertheless, both soluble receptors and antibodies lack important attributes that are critical to function in the IS. Mechanistically, cell surface proteins in the IS can involve the coordinated and often simultaneous interaction of multiple protein targets with a single protein to which they bind. IS interactions occur in close association with the junction of two cells, and a single protein in this structure can interact with both a protein on the same cell (cis) as well as a protein on the associated cell (trans), likely at the same time. Thus, there is a need for improved molecules for modulation of immune responses. Provided are embodiments that meet such needs.

SUMMARY

Provided herein are immunomodulatory proteins that exhibit altered binding affinities to binding partners that are immune protein ligands involved in immunological responses. In some embodiments, the provided immunomodulatory proteins can modulate, such as potentiate or dampen, the activity of the immune protein ligand, thereby modulating immunological responses. In some embodiments, also provided are methods and uses for modulating immune responses by contacting cells expressing one or more of the immune proteins ligands with a provided immunomodulatory protein, for example, in the immunotherapeutic treatment of diseases or conditions that are treatable by modulating of the immune response.

In some embodiments, provided herein is an immunomodulatory protein, comprising at least one non-immunoglobulin affinity modified immunoglobulin superfamily (IgSF) domain comprising one or more amino acid substitution(s) in a wild-type IgSF domain, wherein: the at least one affinity modified IgSF domain has increased binding to at least two cognate binding partners compared to the wild-type IgSF domain; and the at least one affinity modified IgSF domain specifically binds non-competitively to the at least two cognate binding partners. In some embodiments, the at least two cognate binding partners are cell surface molecular species expressed on the surface of a mammalian cell. In some embodiments, the cell surface molecular species are expressed in cis configuration or trans configuration. In some embodiments, the mammalian cell is one of two mammalian cells forming an immunological synapse (IS) and each of the cell surface molecular species is expressed on at least one of the two mammalian cells forming the IS. In some embodiments, at least one of the mammalian cells is a lymphocyte. In some embodiments, the lymphocyte is an NK cell or a T cell. In some embodiments, binding of the affinity modified IgSF domain modulates immunological activity of the lymphocyte.

In some embodiments, the immunomodulatory protein is capable of effecting increased immunological activity compared the wild-type protein comprising the wild-type IgSF domain. In some embodiments, the immunomodulatory protein is capable of effecting decreased immunological activity compared to the wild-type protein comprising the wild-type IgSF domain. In some embodiments, at least one of the mammalian cells is a tumor cell. In some embodiments, the mammalian cells are human cells. In some embodiments, the affinity modified IgSF domain is capable of specifically binding to the two mammalian cells forming the IS.

In some embodiments according to any one of the immunomodulatory proteins described above, the wild-type IgSF domain is from an IgSF family member of a family selected from Signal-Regulatory Protein (SIRP) Family, Triggering Receptor Expressed On Myeloid Cells Like (TREML) Family, Carcinoembryonic Antigen-related Cell Adhesion Molecule (CEACAM) Family, Sialic Acid Binding Ig-Like Lectin (SIGLEC) Family, Butyrophilin Family, B7 family, CD28 family, V-set and Immunoglobulin Domain Containing (VSIG) family, V-set transmembrane Domain (VSTM) family, Major Histocompatibility Complex (MHC) family, Signaling lymphocytic activation molecule (SLAM) family, Leukocyte immunoglobulin-like receptor (LIR), Nectin (Nec) family, Nectin-like (NECL) family, Poliovirus receptor related (PVR) family, Natural cytotoxicity triggering receptor (NCR) family, T cell immunoglobulin and mucin (TIM) family or Killer-cell immunoglobulin-like receptors (KIR) family. In some embodiments, the wild-type IgSF domain is from an IgSF member selected from CD80, CD86, PD-L1, PD-L2, ICOS Ligand, B7-H3, B7-H4, CD28, CTLA4, PD-1, ICOS, BTLA, CD4, CD8-alpha, CD8-beta, LAG3, TIM-3, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, CD200R or Nkp30. In some embodiments, the wild-type IgSF domain is a human IgSF member.

In some embodiments according to any one of the immunomodulatory proteins described above, the wild-type IgSF domain is an IgV domain, an IgC1 domain, an IgC2 domain or a specific binding fragment thereof. In some embodiments, the affinity-modified IgSF domain is an affinity modified IgV domain, affinity modified IgC1 domain or an affinity modified IgC2 domain or is a specific binding fragment thereof comprising the one or more amino acid substitutions.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein comprises at least two non-immunoglobulin affinity modified IgSF domains. In some embodiments each of the non-immunoglobulin affinity modified IgSF domains binds to a different cognate binding partner, wherein the two affinity modified IgSF domain specifically binds non-competitively to the at least two different cognate binding partners. In some embodiments, the at least two non-immunoglobulin affinity modified IgSF domains each comprise one or more different amino acid substitutions in the same wild-type IgSF domain. In some embodiments, the at least two non-immunoglobulin affinity modified IgSF domains each comprise one or more amino acid substitutions in different wild-type IgSF domains. In some embodiments, the different wild-type IgSF domains are from different IgSF family members.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein comprises only one non-immunoglobulin affinity modified IgSF domain.

In some embodiments according to any one of the immunomodulatory proteins described above, the affinity-modified IgSF comprises at least 85% sequence identity to a wild-type IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27. In some embodiments, the immunomodulatory protein further comprises a second affinity-modified IgSF, wherein the second affinity-modified IgSF domain comprises at least 85% sequence identity to a wild-type IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27.

In some embodiments according to any one of the immunomodulatory proteins described above, the wild-type IgSF domain is a member of the B7 family. In some embodiments, the wild-type IgSF domain is a domain of CD80, CD86 or ICOSLG. In some embodiments, the wild-type IgSF domain is a domain of CD80.

In some embodiments according to any one of the immunomodulatory proteins described above, provided herein is an immunomodulatory protein, comprising at least one affinity modified CD80 immunoglobulin superfamily (IgSF) domain comprising one or more amino acid substitution(s) in a wild-type CD80 IgSF domain, wherein the at least one affinity modified CD80 IgSF domain has increased binding to at least two cognate binding partners compared to the wild-type CD80 IgSF domain.

In some embodiments according to any one of the immunomodulatory proteins described above, the cognate binding partners are CD28 and PD-L1. In some embodiments, the wild-type IgSF domain is an IgV domain and/or the affinity modified CD80 domain is an affinity modified IgV domain. In some embodiments, the affinity-modified domain comprises at least 85% sequence identity to a wild-type CD80 domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in SEQ ID NO:1.

In some embodiments according to any one of the immunomodulatory proteins described above, the at least one affinity modified IgSF domain comprises at least 1 and no more than twenty amino acid substitutions in the wild-type IgSF domain. In some embodiments, the at least one affinity modified IgSF domain comprises at least 1 and no more than ten amino acid substitutions in the wild-type IgSF domain. In some embodiments, the at least one affinity modified IgSF domain comprises at least 1 and no more than five amino acid substitutions in the wild-type IgSF domain.

In some embodiments according to any one of the immunomodulatory proteins described above, the affinity modified IgSF domain has at least 120% of the binding affinity as its wild-type IgSF domain to each of the at least two cognate binding partners.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein further comprises a non-affinity modified IgSF domain.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is soluble. In some embodiments, the immunomodulatory protein lacks a transmembrane domain or a cytoplasmic domain. In some embodiments, the immunomodulatory protein comprises only the extracellular domain (ECD) or a specific binding fragment thereof comprising the affinity modified IgSF domain.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is glycosylated or pegylated.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is linked to a multimerization domain. In some embodiments, the immunomodulatory protein is linked to an Fc domain or a variant thereof with reduced effector function. In some embodiments, the Fc domain is an IgG1 domain, an IgG2 domain or is a variant thereof with reduced effector function. In some embodiments, the Fc domain is mammalian, optionally human; or the variant Fc domain comprises one or more amino acid modifications compared to an unmodified Fc domain that is mammalian, optionally human. In some embodiments, the Fc domain or variant thereof comprises the sequence of amino acids set forth in SEQ ID NO:226 or SEQ ID NO:227 or a sequence of amino acids that exhibits at least 85% sequence identity to SEQ ID NO:226 or SEQ ID NO:227.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is linked indirectly via a linker.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is a dimer.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is attached to a liposomal membrane.

Also provided are immunomodulatory proteins comprising at least two non-immunoglobulin immunoglobulin superfamily (IgSF) domains, wherein: at least one is an affinity modified IgSF domain and the at least two non-immunoglobulin IgSF domains each independently bind to at least one different binding partner. In some embodiments, the at least two non-immunoglobulin IgSF domains bind non-competitively to the different binding partners. In some embodiments, the affinity modified IgSF domain contains one more amino acid substitutions in a first wild-type or unmodified IgSF domain. In some embodiments, the other of the IgSF domain is a wild-type or unmodified IgSF domain. In some embodiments, the other of the IgSF domain is also an affinity modified IgSF domain.

In some embodiments according to any of the above immunomodulatory proteins, the immunomodulatory protein contains at least two affinity modified non-immunoglobulin IgSF domains (a first affinity modified IgSF domain and a second affinity modified IgSF domain) in which the first non-immunoglobulin modified IgSF domain comprises one or more amino acid substitutions in a first wild-type-type IgSF domain and the second non-immunoglobulin modified IgSF domain comprises one or more amino acid substitutions in a second wild-type IgSF domain, and in which the first and second non-immunoglobulin modified IgSF domain each specifically bind to at least one different cognate binding partner. In some embodiments, the at least two non-immunoglobulin IgSF domains bind non-competitively to the different binding partners. In some embodiments, the first and second non-immunoglobulin modified IgSF domain is affinity-modified to exhibit altered binding to its cognate binding partner. Thus, in some embodiments, the first and second non-immunoglobulin modified IgSF domains are affinity-modified IgSF domains. In some embodiments, the first non-immunoglobulin modified IgSF domain exhibits altered binding to at least one of its cognate binding partner(s) compared to the first wild-type IgSF domain; and the second non-immunoglobulin modified IgSF domain exhibits altered binding to at least one of its cognate binding partner(s) compared to the second wild-type IgSF domain. In some embodiments, the altered binding is independently either increased or decreased.

In some embodiments, the different cognate binding partners are cell surface molecular species expressed on the surface of a mammalian cell. In some embodiments, the different cell surface molecular species are expressed in cis configuration or trans configuration. In some embodiments, the mammalian cell is one of two mammalian cells forming an immunological synapse (IS) and the different cell surface molecular species is expressed on at least one of the two mammalian cells forming the IS. In some embodiments, at least one of the mammalian cells is a lymphocyte. In some embodiments, the lymphocyte is an NK cell or a T cell. In some embodiments, binding of the immunomodulatory protein to the cell modulates the immunological activity of the lymphocyte. In some embodiments, the immunomodulatory protein is capable of effecting increased immunological activity compared to the wild-type protein comprising the wild-type IgSF domain. In some embodiments, the immunomodulatory protein is capable of effecting decreased immunological activity compared to the wild-type protein comprising the wild-type IgSF domain. In some embodiments, at least one of the mammalian cells is a tumor cell. In some embodiments, the mammalian cells are human cells. In some embodiments, the immunomodulatory protein is capable of specifically binding to the two mammalian cells forming the IS.

In some embodiments according to any one of the immunomodulatory proteins described above, the first and second modified IgSF domains each comprise one or more amino acid substitutions in different wild-type IgSF domains. In some embodiments, the different wild-type IgSF domains are from different IgSF family members. In some embodiments, the first and second modified IgSF domains are non-wild-type combinations. In some embodiments, the first wild-type IgSF domain and second wild-type IgSF domain each individually is from an IgSF family member of a family selected from Signal-Regulatory Protein (SIRP) Family, Triggering Receptor Expressed On Myeloid Cells Like (TREML) Family, Carcinoembryonic Antigen-related Cell Adhesion Molecule (CEACAM) Family, Sialic Acid Binding Ig-Like Lectin (SIGLEC) Family, Butyrophilin Family, B7 family, CD28 family, V-set and Immunoglobulin Domain Containing (VSIG) family, V-set transmembrane Domain (VSTM) family, Major Histocompatibility Complex (MHC) family, Signaling lymphocytic activation molecule (SLAM) family, Leukocyte immunoglobulin-like receptor (LIR), Nectin (Nec) family, Nectin-like (NECL) family, Poliovirus receptor related (PVR) family, Natural cytotoxicity triggering receptor (NCR) family, T cell immunoglobulin and mucin (TIM) family or Killer-cell immunoglobulin-like receptors (KIR) family. In some embodiments, the first wild-type IgSF domain and second wild-type IgSF domain each individually is from an IgSF member selected from CD80, CD86, PD-L1, PD-L2, ICOS Ligand, B7-H3, B7-H4, CD28, CTLA4, PD-1, ICOS, BTLA, CD4, CD8-alpha, CD8-beta, LAG3, TIM-3, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, CD200R or Nkp30.

In some embodiments according to any one of the immunomodulatory proteins described above, the first modified IgSF domain and the second modified IgSF domain each individually comprises at least 85% sequence identity to a wild-type IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27.

In some embodiments according to any one of the immunomodulatory proteins described above, the first and second wild-type IgSF domain each individually is a member of the B7 family. In some embodiments, the first and second wild-type IgSF domain each individually is from CD80, CD86 or ICOSLG. In some embodiments, the first or second wild-type IgSF domain is from a member of the B7 family and the other of the first or second wild-type IgSF domain is from another IgSF family.

In some embodiments according to any one of the immunomodulatory proteins described above, the first and second wild-type IgSF domain is from ICOSLG and NKp30.

In some embodiments according to any one of the immunomodulatory proteins described above, the first and second wild-type IgSF domain is from CD80 and NKp30.

In some embodiments according to any one of the immunomodulatory proteins described above, the first and second wild-type IgSF domain each individually is a human IgSF member.

In some embodiments according to any one of the immunomodulatory proteins described above, the first and second wild-type IgSF domain each individually is an IgV domain, and IgC1 domain, an IgC2 domain or a specific binding thereof. In some embodiments, the first non-immunoglobulin modified domain and the second non-immunoglobulin modified domain each individually is a modified IgV domain, modified IgC1 domain or a modified IgC2 domain or is a specific binding fragment thereof comprising the one or more amino acid substitutions. In some embodiments, at least one of the first non-immunoglobulin modified domain or the second non-immunoglobulin modified domain is a modified IgV domain. In some embodiments, the first non-immunoglobulin modified IgSF domain and the second non-immunoglobulin modified IgSF domain each individually comprise 1 and no more than twenty amino acid substitutions. In some embodiments, the first non-immunoglobulin modified IgSF domain and the second non-immunoglobulin modified IgSF domain each individually comprise 1 and no more than ten amino acid substitutions. In some embodiments, the first non-immunoglobulin modified IgSF domain and the second non-immunoglobulin modified IgSF domain each individually comprise 1 and no more than five amino acid substitutions.

In some embodiments according to any one of the immunomodulatory proteins described above, at least one of the first or second non-immunoglobulin modified IgSF domain has between 10% and 90% of the binding affinity of the wild-type IgSF domain to at least one of its cognate binding partner. In some embodiments, at least one of the first of second non-immunoglobulin modified IgSF domain has at least 120% of the binding affinity of the wild-type IgSF domain to at least one of its cognate binding partner.

In some embodiments according to any one of the immunomodulatory proteins described above, the first and second non-immunoglobulin modified IgSF domain each individually has at least 120% of the binding affinity of the wild-type IgSF domain to at least one of its cognate binding partner.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is soluble.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is glycosylated or pegylated.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is linked to a multimerization domain. In some embodiments, the immunomodulatory protein is linked to an Fc domain or a variant thereof with reduced effector function. In some embodiments, the Fc domain is an IgG1 domain, an IgG2 domain or is a variant thereof with reduced effector function. In some embodiments, the Fc domain is mammalian, optionally human; or the variant Fc domain comprises one or more amino acid modifications compared to an unmodified Fc domain that is mammalian, optionally human. In some embodiments, the Fc domain or variant thereof comprises the sequence of amino acids set forth in SEQ ID NO:226 or SEQ ID NO:227 or a sequence of amino acids that exhibits at least 85% sequence identity to SEQ ID NO:226 or SEQ ID NO:227.

In some embodiments according to any one of the immunomodulatory proteins described above, the variant CD80 polypeptide is linked indirectly via a linker.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is a dimer.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein further comprises one or more additional non-immunoglobulin IgSF domain that is the same of different from the first or second non-immunoglobulin modified IgSF domain. In some embodiments, the one or more additional non-immunoglobulin IgSF domain is an affinity modified IgSF domain.

In some embodiments according to any one of the immunomodulatory proteins described above, the immunomodulatory protein is attached to a liposomal membrane.

In some embodiments, provided herein is a nucleic acid molecule, encoding the immunomodulatory polypeptide according to any one of the embodiments described above. In some embodiments, the nucleic acid molecule is synthetic nucleic acid. In some embodiments, the nucleic acid molecule is cDNA.

In some embodiments, provided herein is a vector, comprising the nucleic acid molecule according to any one of the embodiments described above. In some embodiments, the vector is an expression vector.

In some embodiments, provided herein is a cell, comprising the vector of according to any one of the embodiments described above. In some embodiments, the cell is a eukaryotic cell or prokaryotic cell.

In some embodiments, provided herein is a method of producing an immunomodulatory protein, comprising introducing the nucleic acid molecule according to any one of the embodiments described above or vector according to any one of the embodiments described above into a host cell under conditions to express the protein in the cell. In some embodiments, the method further comprises isolating or purifying the immunomodulatory protein from the cell.

In some embodiments, provided herein is a pharmaceutical composition, comprising the immunomodulatory protein according to any one of the embodiments described above. In some embodiments, the pharmaceutical composition comprises a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical composition is sterile.

In some embodiments, provided herein is an article of manufacture comprising the pharmaceutical composition according to any one of the embodiments described above in a vial. In some embodiments, the vial is sealed.

In some embodiments, provided herein is a kit comprising the pharmaceutical composition according to any one of the embodiments described above, and instructions for use.

In some embodiments, provided herein is a kit comprising the article of manufacture according to any one of the embodiments described above, and instructions for use.

In some embodiments, provided herein is a method of modulating an immune response in a subject, comprising administering therapeutically effective amount of the immunomodulatory protein according to any one of the embodiments described above to the subject. In some embodiments, modulating the immune response treats a disease or condition in the subject. In some embodiments, the immune response is increased. In some embodiments, the disease or condition is a tumor or cancer. In some embodiments, the disease or condition is selected from melanoma, lung cancer, bladder cancer or a hematological malignancy. In some embodiments, the immune response is decreased. In some embodiments, the disease or condition is an inflammatory disease or condition. In some embodiments, the disease or condition is selected from Crohn's disease, ulcerative colitis, multiple sclerosis, asthma, rheumatoid arthritis, or psoriasis.

In some embodiments, provided herein is a method of identifying an affinity modified immunomodulatory protein, comprising: a) contacting a modified protein comprising at least one non-immunoglobulin modified immunoglobulin superfamily (IgSF) domain or specific binding fragment thereof with at least two cognate binding partners under conditions capable of effecting binding of the protein with the at least two cognate binding partners, wherein the at least one modified IgSF domain comprises one or more amino acid substitutions in a wild-type IgSF domain; b) identifying a modified protein comprising the modified IgSF domain that has increased binding to at least one of the two cognate binding partners compared to a protein comprising the wild-type IgSF domain; and c) selecting a modified protein comprising the modified IgSF domain that binds non-competitively to the at least two cognate binding partners, thereby identifying the affinity modified immunomodulatory protein. In some embodiments, step b) comprises identifying a modified protein comprising a modified IgSF domain that has increased binding to each of the at least two cognate binding partners compared to a protein comprising the wild-type domain. In some embodiments, prior to step a), introducing one or more amino acid substitutions into the wild-type IgSF domain, thereby generating a modified protein comprising the modified IgSF domain. In some embodiments, the modified protein comprises at least two modified IgSF domains or specific binding fragments thereof, wherein the first IgSF domain comprises one or more amino acid substitutions in a first wild-type-type IgSF domain and the second non-immunoglobulin affinity modified IgSF domain comprises one or more amino acid substitutions in a second wild-type IgSF domain. In some embodiments, the first and second non-immunoglobulin affinity modified IgSF domain each specifically bind to at least one different cognate binding partner.

In some embodiments, also provided are immunomodulatory protein comprising at least one non-immunoglobulin affinity modified immunoglobulin superfamily (IgSF) domain. In some embodiments, the affinity modified IgSF domain specifically binds non-competitively to at least two cell-surface molecular species. In some embodiments, each of the molecular species is expressed on at least one of two mammalian cells forming an immunological synapse (IS). In some embodiments, the molecular species are in cis configuration or trans configuration. In some embodiments, one of the mammalian cells is a lymphocyte and binding of the affinity modified IgSF domain modulates immunological activity of the lymphocyte. In some embodiments, the affinity modified IgSF domain specifically binds to the two mammalian cells forming the IS.

In some embodiments, the immunomodulatory protein comprises at least two non-immunoglobulin affinity modified IgSF domains and the immunomodulatory protein specifically binds to the two mammalian cells forming the IS. In some embodiments, the immunomodulatory protein comprises at least two affinity modified IgSF domains, wherein the affinity modified IgSF domains are not the same species of IgSF domain.

In some embodiments, one of the two mammalian cells is a tumor cell. In some embodiments, the lymphocyte is an NK cell or a T-cell. In some embodiments, the mammalian cells are a mouse, rat, cynomolgus monkey, or human cells.

In some embodiments, the IgSF cell surface molecular species are human IgSF members.

In some embodiments, the immunomodulatory protein comprises an affinity modified mammalian IgSF member. In some embodiments, the affinity modified IgSF domain is an affinity modified IgV, IgC1, or IgC2 domain. In some embodiments, the affinity modified IgSF domain differs by at least one and no more than ten amino acid substitutions from its wild-type IgSF domain. In some embodiments, the affinity modified IgSF domain differs by at least one and no more than five amino acid substitutions from its wild-type IgSF domain.

In some embodiments, the affinity modified human IgSF member is at least one of: CD80, PVR, ICOSLG, or HAVCR2. In some embodiments, the affinity modified IgSF domain comprises at least one affinity modified human CD80 domain. In some embodiments, the affinity modified IgSF domain is a human CD80 IgSF domain.

In some embodiments, the immunomodulatory protein has at least 85% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-27, or a fragment thereof. In some embodiments, the immunomodulatory protein has at least 90% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-27 or a fragment thereof. In some embodiments, the immunomodulatory protein has at least 95% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-27, or a fragment thereof. In some embodiments, the immunomodulatory protein has at least 99% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-27, or a fragment thereof. In some embodiments, the immunomodulatory protein having at least 85%, 90%, 95%, or 99% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-27 or a fragment thereof further comprises a second immunomodulatory protein, wherein the second immunomodulatory protein has at least 85%, 90%, 95%, or 99% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-27 or a fragment thereof.

In some embodiments, the immunological activity is enhanced. In others it's suppressed.

In some embodiments, the affinity modified IgSF domain has between 10% and 90% of the binding affinity of the wild-type IgSF domain to at least one of the two cell surface molecular species. In some embodiments, the affinity modified IgSF domain specifically binds non-competitively to exactly one IgSF member. In some embodiments, the affinity modified IgSF domain has at least 120% of the binding affinity as its wild-type IgSF domain to at least one of the two cell surface molecular species.

In some embodiments, the immunomodulatory protein is covalently bonded, directly or indirectly, to an antibody fragment crystallizable (Fc). In some embodiments, the immunomodulatory protein is glycosylated or pegylated. In some embodiments, the immunomodulatory protein is soluble. In some embodiments, the immunomodulatory protein is embedded in a liposomal membrane. In some embodiments, the immunomodulatory protein is dimerized by intermolecular disulfide bonds.

In some embodiments, the immunomodulatory protein is in a pharmaceutically acceptable carrier.

In another aspect, provided herein are immunomodulatory protein comprising at least two non-immunoglobulin affinity modified immunoglobulin superfamily (IgSF) domains. The affinity modified IgSF domains each specifically binds to its own cell surface molecular species. Each of the molecular species is expressed on at least one of the two mammalian cells forming an immunological synapse (IS) and one of the mammalian cells is a lymphocyte. The molecular species are, in some embodiments, in cis configuration or trans configuration. Binding of the affinity modified IgSF domain modulates immunological activity of the lymphocyte. In some embodiments, at least one of the affinity modified IgSF domains binds competitively. In some embodiments, the affinity modified IgSF domains are not the same species of IgSF domain. In some embodiments, the affinity modified IgSF domains are non-wild type combinations. In some embodiments, the cell surface molecular species are human IgSF members. In some embodiments, the at least two affinity modified IgSF domains are from at least one of: CD80, CD86, CD274, PDCD1LG2, ICOSLG, CD276, VTCN1, CD28, CTLA4, PDCD1, ICOS, BTLA, CD4, CD8A, CD8B, LAG3, HAVCR2, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, NKp30, or CD200R1.

In some embodiments, the immunomodulatory protein comprises at least two affinity modified mammalian IgSF members. In some embodiments, the mammalian IgSF members are human IgSF members. In some embodiments, the mammalian IgSF members are at least two of: CD80, CD86, CD274, PDCD1LG2, ICOSLG, CD276, VTCN1, CD28, CTLA4, PDCD1, ICOS, BTLA, CD4, CD8A, CD8B, LAG3, HAVCR2, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, NKp30, or CD200R1. In some embodiments, immunological activity is enhanced. In some embodiments, immunological activity is suppressed. In some embodiments, one of the two mammalian cells is a tumor cell. In some embodiments, the lymphocyte is an NK cell or a T-cell. In some embodiments, the mammalian cells are a mouse, rat, cynomolgus monkey, or human cells. In some embodiments, at least one of the two affinity modified IgSF domains has between 10% and 90% of the binding affinity of the wild-type IgSF domain to at least one of the cell surface molecular species. In some embodiments, at least one of the two affinity modified IgSF domains specifically binds to exactly one cell surface molecular species. In some embodiments, at least one of the two affinity modified IgSF domains has at least 120% of the binding affinity as its wild-type IgSF domain to at least one of the two cell surface molecular species. In some embodiments, the affinity modified IgSF domains are at least one of an IgV, IgC1, or IgC2 domain. In some embodiments, each of the at least two affinity modified IgSF domains differs by at least one and no more than ten amino acid substitutions from its wild-type IgSF domain. In some embodiments, each of the at least two affinity modified IgSF domains differs by at least one and no more than five amino acid substitutions from its wild-type IgSF domain. In some embodiments, the immunomodulatory protein is covalently bonded, directly or indirectly, to an antibody fragment crystallizable (Fc). In some embodiments, the immunomodulatory protein is in a pharmaceutically acceptable carrier. In some embodiments, the immunomodulatory protein is glycosylated or pegylated. In some embodiments, the immunomodulatory protein is soluble. In some embodiments, the immunomodulatory protein is embedded in a liposomal membrane. In some embodiments, the immunomodulatory protein is dimerized by intermolecular disulfide bonds.

In another aspect, the present invention relates to a recombinant nucleic acid encoding any of the immunomodulatory proteins summarized above.

In another aspect, the present invention relates to a recombinant expression vector comprising a nucleic acid encoding any of the immunomodulatory proteins summarized above.

In another aspect, the present invention relates to a recombinant host cell comprising an expression vector as summarized above.

In another aspect, the present invention relates to a method of making any of the immunomodulatory proteins summarized above. The method comprises culturing the recombinant host cell under immunomodulatory protein expressing conditions, expressing the immunomodulatory protein encoded by the recombinant expression vector therein, and purifying the recombinant immunomodulatory protein expressed thereby.

In another aspect, the present invention relates to a method of treating a mammalian patient in need of an enhanced or suppressed immunological response by administering a therapeutically effective amount of an immunomodulatory protein of any of the embodiments described above. In some embodiments, the enhanced immunological response treats melanoma, lung cancer, bladder cancer, or a hematological malignancy in the patient. In some embodiments, the suppressed immunological response treats Crohn's disease, ulcerative colitis, multiple sclerosis, asthma, rheumatoid arthritis, or psoriasis in the patient.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A depicts results of a competition binding assay for binding of biotinylated recombinant CD28 Fc fusion protein (rCD28.Fc) to immobilized CD80 variant A91G ECD-Fc fusion molecule in the presence of unlabeled recombinant human PD-L1-his, human CTLA-4-his or human-PD-L2-Fc fusion protein.

FIG. 1B depicts results of a competition binding assay for binding of biotinulated recombinant human PD-L1-his monomeric protein to immobilized CD80 variant A91G ECD-Fc fusion molecule in the presence of unlabeled recombinant human rCD28.Fc, human CTLA-4.Fc or human PD-L2.Fc

INCORPORATION BY REFERENCE

All publications, including patents, patent applications scientific articles and databases, mentioned in this specification are herein incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, including patent, patent application, scientific article or database, were specifically and individually indicated to be incorporated by reference. If a definition set forth herein is contrary to or otherwise inconsistent with a definition set forth in the patents, applications, published applications and other publications that are herein incorporated by reference, the definition set forth herein prevails over the definition that is incorporated herein by reference.

DETAILED DESCRIPTION

Provided herein are soluble immunomodulatory proteins that are capable of binding to one or more protein ligands, and generally two or more protein ligands, to modulate, e.g. induce, enhance or suppress, immunological immune responses. In some embodiments, the protein ligands are cell surface proteins expressed by immune cells that engage with one or more other immune receptor, e.g. on lymphocytes, to induce inhibitory or activating signals. For example, the interaction of certain receptors on lymphocytes with their cognate cell surface ligands to form an immunological synapse (IS) between antigen-presenting cells (APCs) or target cells and lymphocytes can provide costimulatory or inhibitory signals that can regulate the immune system. In some aspects, the immunomodulatory proteins provided herein can alter the interaction of cell surface protein ligands with their receptors to thereby modulate immune cells, such as T cell, activity.

In some embodiments, under normal physiological conditions, the T cell-mediated immune response is initiated by antigen recognition by the T cell receptor (TCR) and is regulated by a balance of co-stimulatory and inhibitory signals (i.e., immune checkpoint proteins). The immune system relies on immune checkpoints to prevent autoimmunity (i.e., self-tolerance) and to protect tissues from excessive damage during an immune response, for example during an attack against a pathogenic infection. In some cases, however, these immunomodulatory proteins can be dysregulated in diseases and conditions, including tumors, as a mechanism for evading the immune system.

Thus, in some aspects, immunotherapy that alters immune cell activity, such as T cell activity, can treat certain diseases and conditions in which the immune response is dysregulated. Therapeutic approaches that seek to modulate interactions in the IS would benefit from the ability to bind multiple IS targets simultaneously and in a manner that is sensitive to temporal sequence and spatial orientation. Current therapeutic approaches fall short of this goal. Instead, soluble receptors and antibodies typically bind no more than a single target protein at a time. This may be due to the absence of more than a single target species. Additionally, wild-type receptors and ligands possess low affinities for cognate binding partners, which preclude their use as soluble therapeutics.

Less trivially, however, soluble receptors and antibodies generally bind competitively (e.g., to no more than one target species at a time) and therefore lack the ability to simultaneously bind multiple targets. And while bispecific antibodies, as well as modalities comprising dual antigen binding regions, can bind to more than one target molecule simultaneously, the three-dimensional configuration typical of these modalities often precludes them intervening in key processes occurring in the IS in a manner consistent with their temporal and spatial requirements.

What is needed is an entirely new class of therapeutic molecules that have the specificity and affinity of antibodies or soluble receptors but, in addition, maintain the size, volume, and spatial orientation constraints required in the IS and possess increased affinity towards respective cognate binding partners. Further, such therapeutics would have the ability to bind to their targets non-competitively as well as competitively. A molecule with these properties would therefore have novel function in the ability to integrate into multi-protein complexes at IS and generate the desired binding configuration and resulting biological activity.

To this end, emerging immuno-oncology therapeutic regimes need to safely break tumor-induced T cell tolerance. Current state-of-the-art immuno-therapeutics block PD-1 or CTLA4, central inhibitory molecules of the B7/CD28 family that are known to limit T cell effector function. While antagonistic antibodies against such single targets function to disrupt immune synapse checkpoint signaling complexes, they fall short of simultaneously activating T cells. Conversely, bispecific antibody approaches activate T cells, but fall short of simultaneously blocking inhibitory ligands that regulate the induced signal.

To address these shortcomings, provided are therapeutic molecules that, in some embodiments, will both stimulate T-cell activation signaling and block inhibitory regulation simultaneously. In some embodiments, the provided immunomodulatory proteins relate to immunoglobulin superfamily (IgSF) components of the immune synapse that are known to have a dual role in both T-cell activation and blocking of inhibitory ligands. In particular aspects, the provided immunomodulatory proteins provide an immunotherapy platform using affinity modified native immune ligands to generate immunotherapy biologics that bind with tunable affinities to one or more of their cognate immune receptors in the treatment of a variety of oncological and immunological indications. In some aspects, IgSF based therapeutics engineered from immune system ligands, such as human immune system ligands, themselves are more likely to retain their ability to normally assemble into key pathways of the immune synapse and maintain normal interactions and regulatory functions in ways that antibodies or next-generation bi-specific reagents cannot. This is due to the relatively large size of antibodies as well as from the fact they are not natural components of the immune synapse. These unique features of human immune system ligands promise to provide a new level of immunotherapeutic efficacy and safety.

The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.

I. Definitions

Unless defined otherwise, all terms of art, notations and other technical and scientific terms or terminology used herein are intended to have the same meaning as is commonly understood by one of ordinary skill in the art to which the claimed subject matter pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art.

The terms used throughout this specification are defined as follows unless otherwise limited in specific instances. As used in the specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms, acronyms, and abbreviations used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Unless indicated otherwise, abbreviations and symbols for chemical and biochemical names is per IUPAC-IUB nomenclature. Unless indicated otherwise, all numerical ranges are inclusive of the values defining the range as well as all integer values in-between.

The term “affinity modified” as used in the context of an immunoglobulin superfamily domain, means a mammalian immunoglobulin superfamily (IgSF) domain having an altered amino acid sequence (relative to the wild-type control IgSF domain) such that it has an increased or decreased binding affinity or avidity to at least one of its cognate binding partners compared to the wild-type (i.e., non-affinity modified) IgSF control domain. In some embodiments, the IgSF domain can contain 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more amino acid differences, such as amino acid substitutions, in a wildtype or unmodified IgSF domain. An IgSF domain having an altered amino acid sequence (relative to the wild-type control IgSF domain) which does not have an increased or decreased binding affinity or avidity to at least one of its cognate binding partners compared to the wild-type IgSF control domain is a non-affinity modified IgSF domain. An increase or decrease in binding affinity or avidity can be determined using well known binding assays such as flow cytometry. Larsen et al., American Journal of Transplantation, Vol 5: 443-453 (2005). See also, Linsley et al., Immunity, 1: 7930801 (1994). An increase in a protein's binding affinity or avidity to its cognate binding partner(s) is to a value at least 10% greater than that of the wild-type IgSF domain control and in some embodiments, at least 20%, 30%, 40%, 50%, 100%, 200%, 300%, 500%, 1000%, 5000%, or 10000% greater than that of the wild-type IgSF domain control value. A decrease in a protein's binding affinity or avidity to at least one of its cognate binding partner is to a value no greater than 90% of the control but no less than 10% of the wild-type IgSF domain control value, and in some embodiments no greater than 80%, 70% 60%, 50%, 40%, 30%, or 20% but no less than 10% of the wild-type IgSF domain control value. An affinity modified protein is altered in primary amino acid sequence by substitution, addition, or deletion of amino acid residues. The term “affinity modified IgSF domain” is not be construed as imposing any condition for any particular starting composition or method by which the affinity modified IgSF domain was created. Thus, the affinity modified IgSF domains of the present invention are not limited to wild type IgSF domains that are then transformed to an affinity modified IgSF domain by any particular process of affinity modification. An affinity modified IgSF domain polypeptide can, for example, be generated starting from wild type mammalian IgSF domain sequence information, then modeled in silico for binding to its cognate binding partner, and finally recombinantly or chemically synthesized to yield the affinity modified IgSF domain composition of matter. In but one alternative example, an affinity modified IgSF domain can be created by site-directed mutagenesis of a wild-type IgSF domain. Thus, affinity modified IgSF domain denotes a product and not necessarily a product produced by any given process. A variety of techniques including recombinant methods, chemical synthesis, or combinations thereof, may be employed.

The terms “binding affinity,” and “binding avidity” as used herein means the specific binding affinity and specific binding avidity, respectively, of a protein for its cognate binding partner under specific binding conditions. In biochemical kinetics avidity refers to the accumulated strength of multiple affinities of individual non-covalent binding interactions, such as between an IgSF domain and its cognate binding partner. As such, avidity is distinct from affinity, which describes the strength of a single interaction. Methods for determining binding affinity or avidity are known in art. See, for example, Larsen et al., American Journal of Transplantation, Vol 5: 443-453 (2005).

The term “biological half-life” refers to the amount of time it takes for a substance, such as an immunomodulatory polypeptide of the present invention, to lose half of its pharmacologic or physiologic activity or concentration. Biological half-life can be affected by elimination, excretion, degradation (e.g., enzymatic) of the substance, or absorption and concentration in certain organs or tissues of the body. In some embodiments, biological half-life can be assessed by determining the time it takes for the blood plasma concentration of the substance to reach half its steady state level (“plasma half-life”). Conjugates that can be used to derivatize and increase the biological half-life of polypeptides of the invention are known in the art and include, but are not limited to, polyethylene glycol (PEG), hydroxyethyl starch (HES), XTEN (extended recombinant peptides; see, WO2013130683), human serum albumin (HSA), bovine serum albumin (BSA), lipids (acylation), and poly-Pro-Ala-Ser (PAS), polyglutamic acid (glutamylation).

The term “cognate binding partner,” in reference to a protein, such as an IgSF domain or an affinity modified IgSF domain, refers to at least one molecule (typically a native mammalian protein) to which the referenced protein specifically binds under specific binding conditions. A species of ligand recognized and specifically binding to its cognate receptor under specific binding conditions is an example of a cognate binding partner of that receptor. A “cognate cell surface binding partner” is a cognate binding partner expressed on a mammalian cell surface. In the present invention a “cell surface molecular species” is a cognate binding partner of the immunological synapse (IS), expressed on and by cells, such as mammalian cells, forming the immunological synapse.

The term “competitive binding” as used herein means that a protein is capable of specifically binding to at least two cognate binding partners but that specific binding of one cognate binding partner inhibits, such as prevents or precludes, simultaneous binding of the second cognate binding partner. Thus, in some cases, it is not possible for a protein to bind the two cognate binding partners at the same time. Generally, competitive binders contain the same or overlapping binding site for specific binding but this is not a requirement. In some embodiments, competitive binding causes a measurable inhibition (partial or complete) of specific binding of a protein to one of its cognate binding partner due to specific binding of a second cognate binding partner. A variety of methods are known to quantify competitive binding such as ELISA (enzyme linked immunosorbent assay) assays.

The term “conservative amino acid substitution” as used herein means an amino acid substitution in which an amino acid residue is substituted by another amino acid residue having a side chain R group with similar chemical properties (e.g., charge or hydrophobicity). Examples of groups of amino acids that have side chains with similar chemical properties include 1) aliphatic side chains: glycine, alanine, valine, leucine, and isoleucine; 2) aliphatic-hydroxyl side chains: serine and threonine; 3) amide-containing side chains: asparagine and glutamine; 4) aromatic side chains: phenylalanine, tyrosine, and tryptophan; 5) basic side chains: lysine, arginine, and histidine; 6) acidic side chains: aspartic acid and glutamic acid; and 7) sulfur-containing side chains: cysteine and methionine. Conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, glutamate-aspartate, and asparagine-glutamine.

The term, “corresponding to” with reference to positions of a protein, such as recitation that nucleotides or amino acid positions “correspond to” nucleotides or amino acid positions in a disclosed sequence, such as set forth in the Sequence listing, refers to nucleotides or amino acid positions identified upon alignment with the disclosed sequence based on structural sequence alignment or using a standard alignment algorithm, such as the GAP algorithm. By aligning the sequences, one skilled in the art can identify corresponding residues, for example, using conserved and identical amino acid residues as guides.

The term “cytokine” includes, e.g., but is not limited to, interleukins, interferons (IFN), chemokines, hematopoietic growth factors, tumor necrosis factors (TNF), and transforming growth factors. In general, these are small molecular weight proteins that regulate maturation, activation, proliferation, and differentiation of cells of the immune system.

The terms “decrease” or “attenuate” “or suppress” as used herein means to decrease by a statistically significant amount. A decrease can be at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%.

The terms “derivatives” or “derivatized” refer to modification of an immunomodulatory protein by covalently linking it, directly or indirectly, so as to alter such characteristics as half-life, bioavailability, immunogenicity, solubility, toxicity, potency, or efficacy while retaining or enhancing its therapeutic benefit. Derivatives can be made by glycosylation, pegylation, lipidation, or Fc-fusion.

As used herein, domain (typically a sequence of three or more, generally 5 or 7 or more amino acids, such as 10 to 200 amino acid residues) refers to a portion of a molecule, such as a protein or encoding nucleic acid, that is structurally and/or functionally distinct from other portions of the molecule and is identifiable. For example, domains include those portions of a polypeptide chain that can form an independently folded structure within a protein made up of one or more structural motifs and/or that is recognized by virtue of a functional activity, such as binding activity. A protein can have one, or more than one, distinct domains. For example, a domain can be identified, defined or distinguished by homology of the primary sequence or structure to related family members, such as homology to motifs. In another example, a domain can be distinguished by its function, such as an ability to interact with a biomolecule, such as a cognate binding partner. A domain independently can exhibit a biological function or activity such that the domain independently or fused to another molecule can perform an activity, such as, for example binding. A domain can be a linear sequence of amino acids or a non-linear sequence of amino acids. Many polypeptides contain a plurality of domains. Such domains are known, and can be identified by those of skill in the art. For exemplification herein, definitions are provided, but it is understood that it is well within the skill in the art to recognize particular domains by name. If needed appropriate software can be employed to identify domains. It is understood that reference to amino acids, including to a specific sequence set forth as a SEQ ID NO used to describe domain organization of an IgSF domain are for illustrative purposes and are not meant to limit the scope of the embodiments provided. It is understood that polypeptides and the description of domains thereof are theoretically derived based on homology analysis and alignments with similar molecules. Thus, the exact locus can vary, and is not necessarily the same for each protein. Hence, the specific IgSF domain, such as specific IgV domain or IgC domain, can be several amino acids (one, two, three or four) longer or shorter.

The term “ectodomain” as used herein refers to the region of a membrane protein, such as a transmembrane protein, that lies outside the vesicular membrane. Ectodomains often comprise binding domains that specifically bind to ligands or cell surface receptors. The ectodomain of a cellular transmembrane protein is alternately referred to as an extracellular domain.

The terms “effective amount” or “therapeutically effective amount” refer to a quantity and/or concentration of a therapeutic composition of the invention, that when administered ex vivo (by contact with a cell from a patient) or in vivo (by administration into a patient) either alone (i.e., as a monotherapy) or in combination with additional therapeutic agents, yields a statistically significant inhibition of disease progression as, for example, by ameliorating or eliminating symptoms and/or the cause of the disease. An effective amount for treating an immune system disease or disorder may be an amount that relieves, lessens, or alleviates at least one symptom or biological response or effect associated with the disease or disorder, prevents progression of the disease or disorder, or improves physical functioning of the patient. In some embodiments the patient is a human patient.

The terms “enhanced” or “increased” as used herein in the context of increasing immunological activity of a mammalian lymphocyte means to increase interferon gamma (IFN-gamma) production, such as by a statistically significant amount. In some embodiments, the immunological activity can be assessed in a mixed lymphocyte reaction (MLR) assay. Methods of conducting MLR assays are known in the art. Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56. In some embodiments an enhancement can be an increase of at least 10%, 20%, 30%, 40%, 50%, 75%, 100%, 200%, 300%, 400%, or 500% greater than a non-zero control value.

The term “host cell” refers to a cell that can be used to express a protein encoded by a recombinant expression vector. A host cell can be a prokaryote, for example, E. coli, or it can be a eukaryote, for example, a single-celled eukaryote (e.g., a yeast or other fungus), a plant cell (e.g., a tobacco or tomato plant cell), an animal cell (e.g., a human cell, a monkey cell, a hamster cell, a rat cell, a mouse cell, or an insect cell) or a hybridoma. Examples of host cells include Chinese hamster ovary (CHO) cells or their derivatives such as Veggie CHO and related cell lines which grow in serum-free media or CHO strain DX-B11, which is deficient in DHFR.

The term “immunological synapse” or “immune synapse” as used herein means the interface between a mammalian cell that expresses MHC I (major histocompatibility complex) or MHC II, such as an antigen-presenting cell or tumor cell, and a mammalian lymphocyte such as an effector T cell or Natural Killer (NK) cell.

The term “immunoglobulin” (abbreviated “Ig”) as used herein is synonymous with the term “antibody” (abbreviated “Ab”) and refers to a mammalian immunoglobulin protein including any of the five human classes: IgA (which includes subclasses IgA1 and IgA2), IgD, IgE, IgG (which includes subclasses IgG1, IgG2, IgG3, and IgG4), and IgM. The term is also inclusive of immunoglobulins that are less than full-length, whether wholly or partially synthetic (e.g., recombinant or chemical synthesis) or naturally produced, such as antigen binding fragment (Fab), variable fragment (Fv) containing V_(H) and V_(L), the single chain variable fragment (scFv) containing V_(H) and V_(L) linked together in one chain, as well as other antibody V region fragments, such as Fab′, F(ab)₂, F(ab′)₂, dsFv diabody, Fc, and Fd polypeptide fragments. Bispecific antibodies, homobispecific and heterobispecific, are included within the meaning of the term.

An Fc (fragment crystallizable) region or domain of an immunoglobulin molecule (also termed an Fc polypeptide) corresponds largely to the constant region of the immunoglobulin heavy chain, and is responsible for various functions, including the antibody's effector function(s). An immunoglobulin Fc fusion (“Fc-fusion”) is a molecule comprising one or more polypeptides (or one or more small molecules) operably linked to an Fc region of an immunoglobulin. An Fc-fusion may comprise, for example, the Fc region of an antibody (which facilitates pharmacokinetics) and the IgSF domain of a wild-type or affinity modified immunoglobulin superfamily domain (“IgSF”), or other protein or fragment thereof. In some embodiments, the Fc additionally facilitates effector functions. In some embodiments, the Fc is a variant Fc that exhibits reduced (e.g. reduced greater than 30%, 40%, 50%, 60%, 70%, 80%, 90% or more) activity to facilitate an effector function. The IgSF domain mediates recognition of the cognate binding partner (comparable to that of antibody variable region of an antibody for an antigen). An immunoglobulin Fc region may be linked indirectly or directly to one or more polypeptides or small molecules (fusion partners). Various linkers are known in the art and can be used to link an Fc to a fusion partner to generate an Fc-fusion. An Fc-fusion protein of the invention typically comprises an immunoglobulin Fc region covalently linked, directly or indirectly, to at least one affinity modified IgSF domain. Fc-fusions of identical species can be dimerized to form Fc-fusion homodimers, or using non-identical species to form Fc-fusion heterodimers.

The term “immunoglobulin superfamily” or “IgSF” as used herein means the group of cell surface and soluble proteins that are involved in the recognition, binding, or adhesion processes of cells. Molecules are categorized as members of this superfamily based on shared structural features with immunoglobulins (i.e., antibodies); they all possess a domain known as an immunoglobulin domain or fold. Members of the IgSF include cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins. They are commonly associated with roles in the immune system. Proteins in the immunological synapse are often members of the IgSF. IgSF can also be classified into “subfamilies” based on shared properties such as function. Such subfamilies typically consist of from 4 to 30 IgSF members.

The terms “IgSF domain” or “immunoglobulin domain” or “Ig domain” as used herein refers a structural domain of IgSF proteins. Ig domains are named after the immunoglobulin molecules. They contain about 70-110 amino acids and are categorized according to their size and function. Ig-domains possess a characteristic Ig-fold, which has a sandwich-like structure formed by two sheets of antiparallel beta strands. Interactions between hydrophobic amino acids on the inner side of the sandwich and highly conserved disulfide bonds formed between cysteine residues in the B and F strands, stabilize the Ig-fold. One end of the Ig domain has a section called the complementarity determining region that is important for the specificity of antibodies for their ligands. The Ig like domains can be classified (into classes) as: IgV, IgC1, IgC2, or IgI. Most Ig domains are either variable (IgV) or constant (IgC). IgV domains with 9 beta strands are generally longer than IgC domains with 7 beta strands. Ig domains of some members of the IgSF resemble IgV domains in the amino acid sequence, yet are similar in size to IgC domains. These are called IgC2 domains, while standard IgC domains are called IgC1 domains. T-cell receptor (TCR) chains contain two Ig domains in the extracellular portion; one IgV domain at the N-terminus and one IgC1 domain adjacent to the cell membrane.

The term “IgSF species” as used herein means an ensemble of IgSF member proteins with identical or substantially identical primary amino acid sequence. Each mammalian immunoglobulin superfamily (IgSF) member defines a unique identity of all IgSF species that belong to that IgSF member. Thus, each IgSF family member is unique from other IgSF family members and, accordingly, each species of a particular IgSF family member is unique from the species of another IgSF family member. Nevertheless, variation between molecules that are of the same IgSF species may occur owing to differences in post-translational modification such as glycosylation, phosphorylation, ubiquitination, nitrosylation, methylation, acetylation, and lipidation. Additionally, minor sequence differences within a single IgSF species owing to gene polymorphisms constitute another form of variation within a single IgSF species as do wild type truncated forms of IgSF species owing to, for example, proteolytic cleavage. A “cell surface IgSF species” is an IgSF species expressed on the surface of a cell, generally a mammalian cell.

The term “immunological activity” as used herein in the context of mammalian lymphocytes means their expression of cytokines, such as chemokines or interleukins. Assays for determining enhancement or suppression of immunological activity include MLR assays for interferon-gamma (Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56), SEB (staphylococcal enterotoxin B) T cell stimulation assay (Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56), and anti-CD3 T cell stimulation assays (Li and Kurlander, J Transl Med. 2010: 8: 104). Induction of an immune response results in an increase in immunological activity relative to quiescent lymphocytes. An immunomodulatory protein or affinity modified IgSF domain of the invention can in some embodiments increase or, in alternative embodiments, decrease IFN-gamma (interferon-gamma) expression in a primary T-cell assay relative to a wild-type IgSF member or IgSF domain control. Those of skill will recognize that the format of the primary T-cell assay used to determine an increase in IFN-gamma expression will differ from that employed to assay for a decrease in IFN-gamma expression. In assaying for the ability of an immunomodulatory protein or affinity modified IgSF domain of the invention to decrease IFN-gamma expression in a primary T-cell assay, a Mixed Lymphocyte Reaction (MLR) assay can be used as described in Example 6. Conveniently, a soluble form of an affinity modified IgSF domain of the invention can be employed to determine its ability to antagonize and thereby decrease the IFN-gamma expression in a MLR as likewise described in Example 6. Alternatively, in assaying for the ability of an immunomodulatory protein or affinity modified IgSF domain of the invention to increase IFN-gamma expression in a primary T-cell assay, a co-immobilization assay can be used. In a co-immobilization assay, a T-cell receptor signal, provided in some embodiments by anti-CD3 antibody, is used in conjunction with a co-immobilized affinity modified IgSF domain to determine the ability to increase IFN-gamma expression relative to a wild-type IgSF domain control.

An “immunomodulatory protein” is a protein that modulates immunological activity. By “modulation” or “modulating” an immune response is meant that immunological activity is either enhanced or suppressed. An immunomodulatory protein can be a single polypeptide chain or a multimer (dimers or higher order multimers) of at least two polypeptide chains covalently bonded to each other by, for example, interchain disulfide bonds. Thus, monomeric, dimeric, and higher order multimeric proteins are within the scope of the defined term. Multimeric proteins can be homomultimeric (of identical polypeptide chains) or heteromultimeric (of different polypeptide chains).

The term “increase” as used herein means to increase by a statistically significant amount. An increase can be at least 5%, 10%, 20%, 30%, 40%, 50%, 75%, 100%, or greater than a non-zero control value.

The term “lymphocyte” as used herein means any of three subtypes of white blood cell in a mammalian immune system. They include natural killer cells (NK cells) (which function in cell-mediated, cytotoxic innate immunity), T cells (for cell-mediated, cytotoxic adaptive immunity), and B cells (for humoral, antibody-driven adaptive immunity). T cells include: T helper cells, cytotoxic T-cells, natural killer T-cells, memory T-cells, regulatory T-cells, or gamma delta T-cells. Innate lymphoid cells (ILC) are also included within the definition of lymphocyte.

The terms “mammal,” “subject,” or “patient” specifically includes reference to at least one of a: human, chimpanzee, rhesus monkey, cynomolgus monkey, dog, cat, mouse, or rat.

The terms “modulating” or “modulate” as used herein in the contest of an immune response, such as a mammalian immune response, refer to any alteration, such as an increase or a decrease, of an existing or potential immune responses that occurs as a result of administration of an immunomodulatory protein of the present invention. Thus, it refers to an alteration, such as an increase or decrease, of an immune response as compared to the immune response that occurs or is present in the absence of the administration of the immunomodulatory protein. Such modulation includes any induction, or alteration in degree or extent, or suppression of immunological activity of an immune cell. Immune cells include B cells, T cells, NK (natural killer) cells, NK T cells, professional antigen-presenting cells (APCs), and non-professional antigen-presenting cells, and inflammatory cells (neutrophils, macrophages, monocytes, eosinophils, and basophils). Modulation includes any change imparted on an existing immune response, a developing immune response, a potential immune response, or the capacity to induce, regulate, influence, or respond to an immune response. Modulation includes any alteration in the expression and/or function of genes, proteins and/or other molecules in immune cells as part of an immune response. Modulation of an immune response or modulation of immunological activity includes, for example, the following: elimination, deletion, or sequestration of immune cells; induction or generation of immune cells that can modulate the functional capacity of other cells such as autoreactive lymphocytes, antigen presenting cells, or inflammatory cells; induction of an unresponsive state in immune cells (i.e., anergy); enhancing or suppressing the activity or function of immune cells, including but not limited to altering the pattern of proteins expressed by these cells. Examples include altered production and/or secretion of certain classes of molecules such as cytokines, chemokines, growth factors, transcription factors, kinases, costimulatory molecules, or other cell surface receptors or any combination of these modulatory events. Modulation can be assessed, for example, by an alteration in IFN-gamma (interferon gamma) expression relative to or as compared to the wild-type or unmodified IgSF domain(s) control in a primary T cell assay (see, Zhao and Ji, Exp Cell Res. 2016 Jan. 1; 340(1) 132-138).

The term “molecular species” as used herein means an ensemble of proteins with identical or substantially identical primary amino acid sequence. Each mammalian immunoglobulin superfamily (IgSF) member defines a collection of identical or substantially identical molecular species. Thus, for example, human CD80 is an IgSF member and each human CD80 molecule is a species of CD80. Variation between molecules that are of the same molecular species may occur owing to differences in post-translational modification such as glycosylation, phosphorylation, ubiquitination, nitrosylation, methylation, acetylation, and lipidation. Additionally, minor sequence differences within a single molecular species owing to gene polymorphisms constitute another form of variation within a single molecular species as do wild type truncated forms of a single molecular species owing to, for example, proteolytic cleavage. A “cell surface molecular species” is a molecular species expressed on the surface of a mammalian cell. Two or more different species of protein, each of which is present exclusively on one or exclusively the other (but not both) of the two mammalian cells forming the IS, are said to be in “cis” or “cis configuration” with each other. Two different species of protein, the first of which is exclusively present on one of the two mammalian cells forming the IS and the second of which is present exclusively on the second of the two mammalian cells forming the IS, are said to be in “trans” or “trans configuration.” Two different species of protein each of which is present on both of the two mammalian cells forming the IS are in both cis and trans configurations on these cells.

The term “non-competitive binding” as used herein means the ability of a protein to specifically bind simultaneously to at least two cognate binding partners. In some embodiments, the binding occurs under specific binding conditions. Thus, the protein is able to bind to at least two different cognate binding partners at the same time, although the binding interaction need not be for the same duration such that, in some cases, the protein is specifically bound to only one of the cognate binding partners. In some embodiments, the simultaneous binding is such that binding of one cognate binding partner does not substantially inhibit simultaneous binding to a second cognate binding partner. In some embodiments, non-competitive binding means that binding a second cognate binding partner to its binding site on the protein does not displace the binding of a first cognate binding partner to its binding site on the protein. Methods of assessing non-competitive binding are well known in the art such as the method described in Perez de La Lastra et al., Immunology, 1999 April: 96(4): 663-670. In some cases, in non-competitive interactions, the first cognate binding partner specifically binds at an interaction site that does not overlap with the interaction site of the second cognate binding partner such that binding of the second cognate binding partner does not directly interfere with the binding of the first cognate binding partner. Thus, any effect on binding of the cognate binding partner by the binding of the second cognate binding partner is through a mechanism other than direct interference with the binding of the first cognate binding partner. For example, in the context of enzyme-substrate interactions, a non-competitive inhibitor binds to a site other than the active site of the enzyme. Non-competitive binding encompasses uncompetitive binding interactions in which a second cognate binding partner specifically binds at an interaction site that does not overlap with the binding of the first cognate binding partner but binds to the second interaction site only when the first interaction site is occupied by the first cognate binding partner.

The terms “nucleic acid” and “polynucleotide” are used interchangeably to refer to a polymer of nucleic acid residues (e.g., deoxyribonucleotides or ribonucleotides) in either single- or double-stranded form. Unless specifically limited, the terms encompass nucleic acids containing known analogues of natural nucleotides and that have similar binding properties to it and are metabolized in a manner similar to naturally-occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary nucleotide sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues. The term nucleic acid or polynucleotide encompasses cDNA or mRNA encoded by a gene.

The term “pharmaceutical composition” refers to a composition suitable for pharmaceutical use in a mammalian subject, often a human. A pharmaceutical composition typically comprises an effective amount of an active agent (e.g., an immunomodulatory protein of the invention) and a carrier, excipient, or diluent. The carrier, excipient, or diluent is typically a pharmaceutically acceptable carrier, excipient or diluent, respectively.

The terms “polypeptide” and “protein” are used interchangeably herein and refer to a molecular chain of two or more amino acids linked through peptide bonds. The terms do not refer to a specific length of the product. Thus, “peptides,” and “oligopeptides,” are included within the definition of polypeptide. The terms include post-translational modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like. The terms also include molecules in which one or more amino acid analogs or non-canonical or unnatural amino acids are included as can be synthesized, or expressed recombinantly using known protein engineering techniques. In addition, proteins can be derivatized as described herein by well-known organic chemistry techniques.

The term “primary T-cell assay” as used herein refers to an in vitro assay to measure interferon-gamma (“IFN-gamma”) expression. A variety of such primary T-cell assays are known in the art such as that described in Example 6. In a preferred embodiment, the assay used is anti-CD3 coimmobilization assay. In this assay, primary T cells are stimulated by anti-CD3 immobilized with or without additional recombinant proteins. Culture supernatants are harvested at timepoints, usually 24-72 hours. In another embodiment, the assay used is a mixed lymphocyte reaction (MLR). In this assay, primary T cells are simulated with allogenic APC. Culture supernatants are harvested at timepoints, usually 24-72 hours. Human IFN-gamma levels are measured in culture supernatants by standard ELISA techniques. Commercial kits are available from vendors and the assay is performed according to manufacturer's recommendation.

The term “purified” as applied to nucleic acids or immunomodulatory proteins of the invention generally denotes a nucleic acid or polypeptide that is substantially free from other components as determined by analytical techniques well known in the art (e.g., a purified polypeptide or polynucleotide forms a discrete band in an electrophoretic gel, chromatographic eluate, and/or a media subjected to density gradient centrifugation). For example, a nucleic acid or polypeptide that gives rise to essentially one band in an electrophoretic gel is “purified.” A purified nucleic acid or immunomodulatory protein of the invention is at least about 50% pure, usually at least about 75%, 80%, 85%, 90%, 95%, 96%, 99% or more pure (e.g., percent by weight or on a molar basis).

The term “recombinant” indicates that the material (e.g., a nucleic acid or a polypeptide) has been artificially (i.e., non-naturally) altered by human intervention. The alteration can be performed on the material within, or removed from, its natural environment or state. For example, a “recombinant nucleic acid” is one that is made by recombining nucleic acids, e.g., during cloning, affinity modification, DNA shuffling or other well-known molecular biological procedures. A “recombinant DNA molecule,” is comprised of segments of DNA joined together by means of such molecular biological techniques. The term “recombinant protein” or “recombinant polypeptide” as used herein refers to a protein molecule (e.g., an immunomodulatory protein) which is expressed using a recombinant DNA molecule. A “recombinant host cell” is a cell that contains and/or expresses a recombinant nucleic acid. Transcriptional control signals in eukaryotes comprise “promoter” and “enhancer” elements. Promoters and enhancers consist of short arrays of DNA sequences that interact specifically with cellular proteins involved in transcription. Promoter and enhancer elements have been isolated from a variety of eukaryotic sources including genes in yeast, insect and mammalian cells and viruses (analogous control elements, i.e., promoters, are also found in prokaryotes). The selection of a particular promoter and enhancer depends on what cell type is to be used to express the protein of interest. The terms “in operable combination,” “in operable order” and “operably linked” as used herein refer to the linkage of nucleic acid sequences in such a manner or orientation that a nucleic acid molecule capable of directing the transcription of a given gene and/or the synthesis of a desired protein molecule is produced. The term also refers to the linkage of amino acid sequences in such a manner so that a functional protein is produced and/or transported.

The term “recombinant expression vector” as used herein refers to a DNA molecule containing a desired coding sequence (e.g., an immunomodulatory nucleic acid) and appropriate nucleic acid sequences necessary for the expression of the operably linked coding sequence in a particular host cell. Nucleic acid sequences necessary for expression in prokaryotes include a promoter, optionally an operator sequence, a ribosome binding site and possibly other sequences. Eukaryotic cells are known to utilize promoters, enhancers, and termination and polyadenylation signals. A secretory signal peptide sequence can also, optionally, be encoded by the recombinant expression vector, operably linked to the coding sequence for the inventive recombinant fusion protein, so that the expressed fusion protein can be secreted by the recombinant host cell, for more facile isolation of the fusion protein from the cell, if desired.

The term “sequence identity” as used herein refers to the sequence identity between genes or proteins at the nucleotide or amino acid level, respectively. “Sequence identity” is a measure of identity between proteins at the amino acid level and a measure of identity between nucleic acids at nucleotide level. The protein sequence identity may be determined by comparing the amino acid sequence in a given position in each sequence when the sequences are aligned. Similarly, the nucleic acid sequence identity may be determined by comparing the nucleotide sequence in a given position in each sequence when the sequences are aligned. Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. The BLAST algorithm calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Center for Biotechnology Information (NCBI) website.

The term “soluble” as used herein in reference to proteins, means that the protein is not a membrane protein. In general, a soluble protein contains only the extracellular domain of an IgSF family member receptor, or a portion thereof containing an IgSF domain or domains or specific-binding fragments thereof.

The term “species” as used herein in the context of a nucleic acid sequence or a polypeptide sequence refers to an identical collection of such sequences. Slightly truncated sequences that differ (or encode a difference) from the full length species at the amino-terminus or carboxy-terminus by no more than 1, 2, or 3 amino acid residues are considered to be of a single species. Such microheterogeneities are a common feature of manufactured proteins.

The term “specifically binds” as used herein means the ability of a protein, under specific binding conditions, to bind to a target protein such that its affinity or avidity is at least 10 times as great, but optionally 50, 100, 250 or 500 times as great, or even at least 1000 times as great as the average affinity or avidity of the same protein to a collection of random peptides or polypeptides of sufficient statistical size. A specifically binding protein need not bind exclusively to a single target molecule (e.g., its cognate binding partner) but may specifically bind to a non-target molecule due to similarity in structural conformation between the target and non-target (e.g., paralogs or orthologs). Those of skill will recognize that specific binding to a molecule having the same function in a different species of animal (i.e., ortholog) or to a non-target molecule having a substantially similar epitope as the target molecule (e.g., paralog) is possible and does not detract from the specificity of binding which is determined relative to a statistically valid collection of unique non-targets (e.g., random polypeptides). Thus, an affinity modified polypeptide of the invention may specifically bind to more than one distinct species of target molecule due to cross-reactivity. Generally, such off-target specific binding is mitigated by reducing affinity or avidity for undesired targets. Solid-phase ELISA immunoassays or Biacore measurements can be used to determine specific binding between two proteins. Generally, interactions between two binding proteins have dissociation constants (Kd) less than 1×10⁻⁵ M, and often as low as 1×10⁻¹² M. In certain aspects of the present disclosure, interactions between two binding proteins have dissociation constants of 1×10⁻⁶ M, 1×10⁻⁷ M, 1×10⁻⁸ M, 1×10⁻⁹ M, 1×10⁻¹⁰ M or 1×10⁻¹¹ M.

The term “specific binding fragment” or “fragment” as used herein in reference to a mature (i.e., absent the signal peptide) wild-type IgSF domain, means a polypeptide that is shorter than the full-length mature IgSF domain and that specifically binds in vitro and/or in vivo to the mature wild-type IgSF domain's native cognate binding partner. In some embodiments, the specific binding fragment is at at least 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% the sequence length of the full-length mature wild-type sequence. The specific binding fragment can be altered in sequence to form an affinity modified IgSF domain of the invention. In some embodiments, the specific binding fragment modulates immunological activity of a lymphocyte.

The terms “suppressed” or “decreased” as used herein means to decrease by a statistically significant amount. In some embodiments suppression can be a decrease of at least 10%, and up to 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%.

The term “targeting moiety” as used herein refers to a composition that is covalently or non-covalently attached to, or physically encapsulates, a polypeptide comprising a wild-type and/or affinity modified IgSF domain of the present invention. The targeting moiety has specific binding affinity for a desired cognate binding partner such as a cell surface receptor or a tumor antigen such as tumor specific antigen (TSA) or a tumor associated antigen (TAA). Typically, the desired cognate binding partner is localized on a specific tissue or cell-type. Targeting moieties include: antibodies, antigen binding fragment (Fab), variable fragment (Fv) containing V_(H) and V_(L), the single chain variable fragment (scFv) containing V_(H) and V_(L) linked together in one chain, as well as other antibody V region fragments, such as Fab′, F(ab)₂, F(ab′)₂, dsFv diabody, nanobodies, soluble receptors, receptor ligands, affinity matured receptors or ligands, as well as small molecule (<500 dalton) compositions (e.g., specific binding receptor compositions). Targeting moieties can also be attached covalently or non-covalently to the lipid membrane of liposomes that encapsulate an immunomodulatory polypeptide of the present invention.

The terms “treating,” “treatment,” or “therapy” of a disease or disorder as used herein mean slowing, stopping or reversing the disease or disorders progression, as evidenced by decreasing, cessation or elimination of either clinical or diagnostic symptoms, by administration of an immunomodulatory protein of the present invention either alone or in combination with another compound as described herein. “Treating,” “treatment,” or “therapy” also means a decrease in the severity of symptoms in an acute or chronic disease or disorder or a decrease in the relapse rate as for example in the case of a relapsing or remitting autoimmune disease course or a decrease in inflammation in the case of an inflammatory aspect of an autoimmune disease. As used herein in the context of cancer, the terms “treatment” or, “inhibit,” “inhibiting” or “inhibition” of cancer refers to at least one of: a statistically significant decrease in the rate of tumor growth, a cessation of tumor growth, or a reduction in the size, mass, metabolic activity, or volume of the tumor, as measured by standard criteria such as, but not limited to, the Response Evaluation Criteria for Solid Tumors (RECIST), or a statistically significant increase in progression free survival (PFS) or overall survival (OS). “Preventing,” “prophylaxis,” or “prevention” of a disease or disorder as used in the context of this invention refers to the administration of an immunomodulatory protein of the present invention, either alone or in combination with another compound, to prevent the occurrence or onset of a disease or disorder or some or all of the symptoms of a disease or disorder or to lessen the likelihood of the onset of a disease or disorder.

The term “tumor specific antigen” or “TSA” as used herein refers to an antigen that is present primarily on tumor cells of a mammalian subject but generally not found on normal cells of the mammalian subject. A tumor specific antigen need not be exclusive to tumor cells but the percentage of cells of a particular mammal that have the tumor specific antigen is sufficiently high or the levels of the tumor specific antigen on the surface of the tumor are sufficiently high such that it can be targeted by anti-tumor therapeutics, such as immunomodulatory polypeptides of the invention, and provide prevention or treatment of the mammal from the effects of the tumor. In some embodiments, in a random statistical sample of cells from a mammal with a tumor, at least 50% of the cells displaying a TSA are cancerous. In other embodiments, at least 60%, 70%, 80%, 85%, 90%, 95%, or 99% of the cells displaying a TSA are cancerous.

As used herein, “screening” refers to identification or selection of a molecule or portion thereof from a collection or library of molecules and/or portions thereof, based on determination of the activity or property of a molecule or portion thereof. Screening can be performed in any of a variety of ways, including, for example, by assays assessing direct binding (e.g. binding affinity) of the molecule to a target protein or by functional assays assessing modulation of an activity of a target protein.

The term “wild-type” or “natural” or “native” or “parental” as used herein is used in connection with biological materials such as nucleic acid molecules, proteins, IgSF members, host cells, and the like, refers to those which are found in nature and not modified by human intervention. A wild-type IgSF domain is a type of non-affinity modified IgSF domain. In some embodiments of immunomodulatory proteins of the invention, a non-affinity modified IgSF is a wild-type IgSF domain.

II. Affinity-Modified Immunomodulatory Proteins

The present invention provides immunomodulatory proteins that have therapeutic utility by modulating immunological activity in a mammal with a disease or disorder in which modulation of the immune system response is beneficial.

The IgSF family members included within the scope of the immunomodulatory proteins of the present invention excludes antibodies (i.e., immunoglobulins) such as those that are mammalian or may be of mammalian origin. Thus, the present invention relates to non-immunoglobulin (i.e., non-antibody) IgSF domains. Wild-type mammalian IgSF family members that are not immunoglobulins (i.e. antibodies) are known in the art as are their nucleic and amino acid sequences. All non-immunoglobulin mammalian IgSF family members are included within the scope of the invention.

In some embodiments, the non-immunoglobulin IgSF family members, and the corresponding IgSF domains present therein, are of mouse, rat, cynomolgus monkey, or human origin. In some embodiments, the IgSF family members are members from at least or exactly one, two, three, four, five, or more IgSF subfamilies such as: Signal-Regulatory Protein (SIRP) Family, Triggering Receptor Expressed On Myeloid Cells Like (TREML) Family, Carcinoembryonic Antigen-related Cell Adhesion Molecule (CEACAM) Family, Sialic Acid Binding Ig-Like Lectin (SIGLEC) Family, Butyrophilin Family, B7 family, CD28 family, V-set and Immunoglobulin Domain Containing (VSIG) family, V-set transmembrane Domain (VSTM) family, Major Histocompatibility Complex (MHC) family, Signaling lymphocytic activation molecule (SLAM) family, Leukocyte immunoglobulin-like receptor (LIR), Nectin (Nec) family, Nectin-like (NECL) family, Poliovirus receptor related (PVR) family, Natural cytotoxicity triggering receptor (NCR) family, or Killer-cell immunoglobulin-like receptors (KIR) family.

In some embodiments, non-immunoglobulin IgSF family members, and the corresponding IgSF domains present therein, of an immunomodulatory protein of the invention, are affinity-modified compared to a mammalian IgSF member. In some embodiments, the mammalian IgSF member is one of the IgSF members or comprises an IgSF domain from one of the IgSF members as indicated in Table 1 including any mammalian orthologs thereof. Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution.

The first column of Table 1 provides the name and, optionally, the name of some possible synonyms for that particular IgSF member. The second column provides the protein identifier of the UniProtKB database, a publicly available database accessible via the internet at uniprot.org. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases include the UniProt Knowledgebase (UniProtKB). UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR) and supported mainly by a grant from the U.S. National Institutes of Health (NIH). The third column provides the region where the indicated IgSF domain is located. The region is specified as a range where the domain is inclusive of the residues defining the range. Column 3 also indicates the IgSF domain class for the specified IgSF region. Column 4 provides the region where the indicated additional domains are located (signal peptide, S; extracellular domain, E; transmembrane domain, T; cytoplasmic domain, C). Column 5 indicates for some of the listed IgSF members, some of its cognate cell surface binding partners.

Typically, the affinity modified IgSF domain of the provided embodiments is a human or murine affinity modified IgSF domain.

TABLE 1 IgSF members according to the present disclosure. IgSF Member Amino Acid Cognate Cell Sequence (SEQ ID NO) IgSF UniProtKB Surface Precursor Member Protein IgSF Region & Other Binding (mature (Synonyms) Identifier Domain Class Domains Partners residues) ECD CD80 NP_005182.1 35-138 or S: 1-34, CD28, CTLA4, SEQ ID NO: 1 SEQ ID NO: 28 (B7-1) P33681 37-138 IgV, E: 35-242, PD-L1 (35-288) 145-230 or T: 243-263, 154-232 IgC C: 264-288 CD86 P42081.2 33-131 IgV, S: 1-23, CD28, CTLA4 SEQ ID NO: 2 SEQ ID NO: 29 (B7-2) 150-225 IgC2 E: 24-247, (24-329) T: 248-268, C: 269-329 CD274 Q9NZQ7.1 24-130 IgV, S: 1-18, PD-1, B7-1 SEQ ID NO: 3 SEQ ID NO: 30 (PD-L1, 133-225 IgC2 E: 19-238, (19-290) B7-H1) T: 239-259, C: 260-290 PDCD1LG2 Q9BQ51.2 21-118 IgV, S: 1-19, PD-1, RGMb SEQ ID NO: 4 SEQ ID NO: 31 (PD-L2, 122-203 IgC2 E: 20-220, (20-273) CD273) T: 221-241, C: 242-273 ICOSLG O75144.2 19-129 IgV, S: 1-18, ICOS, CD28, SEQ ID NO: 5 SEQ ID NO: 32 (B7RP1, 141-227 IgC2 E: 19-256, CTLA4 (19-302) CD275, T: 257-277, ICOSL, C: 278-302 B7-H2) CD276 Q5ZPR3.1 29-139 IgV, S: 1-28, SEQ ID NO: 6 SEQ ID NO: 33 (B7-H3) 145-238 IgC2, E: 29-466, (29-534) 243-357 IgV, T: 467-487, 367-453 IgC C: 488-534 VTCN1 Q7Z7D3.1 35-146 IgV, S: 1-24, SEQ ID NO: 7 SEQ ID NO: 34 (B7-H4) 153-241 IgV E: 25-259, (25-282) T: 260-280, C: 281-282 CD28 P10747.1 28-137 IgV S: 1-18, B7-1, B7-2, SEQ ID NO: 8 SEQ ID NO: 35 E: 19-152, B7RP1 (19-220) T: 153-179, C: 180-220 CTLA4 P16410.3 39-140 IgV S: 1-35, B7-1, B7-2, SEQ ID NO: 9 SEQ ID NO: 36 E: 36-161, B7RP1 (36-223) T: 162-182, C: 183-223 PDCD1 Q15116.3 35-145 IgV S: 1-20, PD-L1, PD-L2 SEQ ID NO: 10 SEQ ID NO: 37 (PD-1) E: 21-170, (21-288) T: 171-191, C: 192-288 ICOS Q9Y6W8.1 30-132 IgV S: 1-20, B7RP1 SEQ ID NO: 11 SEQ ID NO: 38 E: 21-140, (21-199) T: 141-161, C: 162-199 BTLA Q7Z6A9.3 31-132 IgV S: 1-30, HVEM SEQ ID NO: 12 SEQ ID NO: 39 (CD272) E: 31-157, (31-289) T: 158-178, C: 179-289 CD4 P01730.1 26-125 IgV, S: 1-25, MHC class II SEQ ID NO: 13 SEQ ID NO: 40 126-203 IgC2, E: 26-396, (26-458) 204-317 IgC2, T: 397-418, 317-389 IgC2 C: 419-458 CD8A P01732.1 22-135 IgV S: 1-21, MHC class I SEQ ID NO: 14 SEQ ID NO: 41 (CD8-alpha) E: 22-182, (22-235) T: 183-203, C: 204-235 CD8B P10966.1 22-132 IgV S: 1-21, MHC class I SEQ ID NO: 15 SEQ ID NO: 42 (CD8-beta) E: 22-170, (22-210) T: 171-191, C: 192-210 LAG3 P18627.5 37-167 IgV, S: 1-28, MHC class II SEQ ID NO: 16 SEQ ID NO: 43 168-252 IgC2, E: 29-450, (29-525) 265-343 IgC2, T: 451-471, 349-419 IgC2 C: 472-525 HAVCR2 Q8TDQ0.3 22-124 IgV S: 1-21, CEACAM-1, SEQ ID NO: 17 SEQ ID NO: 44 (TIM-3) E: 22-202, phosphatidylserine, (22-301) T: 203-223, Galectin-9, C: 224-301 HMGB1 CEACAM1 P13688.2 35-142 IgV, S: 1-34, TIM-3 SEQ ID NO: 18 SEQ ID NO: 45 145-232 IgC2, E: 35-428, (35-526) 237-317 IgC2, T: 429-452, 323-413 IgC C: 453-526 TIGIT Q495A1.1 22-124 IgV S: 1-21, CD155, CD112 SEQ ID NO: 19 SEQ ID NO: 46 E: 22-141, (22-244) T: 142-162, C: 163-244 PVR P15151.2 24-139 IgV, S: 1-20, TIGIT, CD226, SEQ ID NO: 20 SEQ ID NO: 47 (CD155) 145-237 IgC2, E: 21-343, CD96, poliovirus (21-417) 244-328 IgC2 T: 344-367, C: 368-417 PVRL2 Q92692.1 32-156 IgV, S: 1-31, TIGIT, CD226, SEQ ID NO: 21 SEQ ID NO: 48 (CD112) 162-256 IgC2, E: 32-360, CD112R (32-538) 261-345 IgC2 T: 361-381, C: 382-538 CD226 Q15762.2 19-126 IgC2, S: 1-18, CD155, CD112 SEQ ID NO: 22 SEQ ID NO: 49 135-239 IgC2 E: 19-254, (19-336) T: 255-275, C: 276-336 CD2 P06729.2 25-128 IgV, S: 1-24, CD58 SEQ ID NO: 23 SEQ ID NO: 50 129-209 IgC2 E: 25-209, (25-351) T: 210-235, C: 236-351 CD160 O95971.1 27-122 IgV N/A HVEM, MHC SEQ ID NO: 24 SEQ ID NO: 51 family of proteins (27-159) CD200 P41217.4 31-141 IgV, S: 1-30, CD200R SEQ ID NO: 25 SEQ ID NO: 52 142-232 IgC2 E: 31-232, (31-278) T: 233-259, C: 260-278 CD200R1 Q8TD46.2 53-139 IgV, S: 1-28, CD200 SEQ ID NO: 26 SEQ ID NO: 53 (CD200R) 140-228 IgC2 E: 29-243, (29-325) T: 244-264, C: 265-325 NCR3 O14931.1 19-126 IgC-like S: 1-18, B7-H6 SEQ ID NO: 27 SEQ ID NO: 54 (NKp30) E: 19-135, (19-201) T: 136-156, C: 157-201

In some embodiments, the immunomodulatory proteins of the present invention comprise at least one affinity modified mammalian IgSF domain. The affinity modified IgSF domain can be affinity modified to specifically bind to a single or multiple (2, 3, 4, or more) cognate binding partners (also called a “counter structure ligand”). An IgSF domain can be affinity modified to independently increase or decrease specific binding affinity or avidity to each of the multiple cognate binding partners to which it binds. By this mechanism, specific binding to each of multiple cognate binding partners is independently tuned to a particular affinity or avidity.

In some embodiments, the cognate binding partner of an IgSF domain is at least one, and sometimes at least two or three of the cognate binding partners of the wild-type IgSF domain, such as those listed in Table 1. The sequence of the IgSF domain, such as a mammalian IgSF domain, is affinity modified by altering its sequence with at least one substitution, addition, or deletion. Alteration of the sequence can occur at the binding site for the cognate binding partner or at an allosteric site. In some embodiments, a nucleic acid encoding a IgSF domain, such as a mammalian IgSF domain, is affinity modified by substitution, addition, deletion, or combinations thereof, of specific and pre-determined nucleotide sites to yield a nucleic acid of the invention. In some contrasting embodiments, a nucleic acid encoding an IgSF domain, such as a mammalian IgSF domain, is affinity modified by substitution, addition, deletion, or combinations thereof, at random sites within the nucleic acid. In some embodiments, a combination of the two approaches (pre-determined and random) is utilized. In some embodiments, design of the affinity modified IgSF domains of the present invention is performed in silico.

In some embodiments, the affinity modified IgSF domain contains one or more amino acid substitutions (alternatively, “mutations” or “replacements”) relative to a wild-type or unmodified polypeptide or a portion thereof containing an immunoglobulin superfamily (IgSF) domain, such as an IgV domain or an IgC domain or specific binding fragment of the IgV domain or the IgC domain. In some embodiments, the immunomodulatory protein comprises an affinity modified IgSF domain that contains an IgV domain or an IgC domain or specific binding fragments thereof in which the at least one of the amino acid substitutions is in the IgV domain or IgC domain or a specific binding fragment thereof. In some embodiments, by virtue of the altered binding activity or affinity, the IgV domain or IgC domain is an affinity-modified IgSF domain.

In some embodiments, the IgSF domain, such as a mammalian IgSF domain, is affinity modified in sequence with at least one but no more than a total of 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions, additions, deletions, or combinations thereof. In some embodiments, the IgSF domain, such as a mammalian IgSF domain, is affinity modified in sequence with at least one but no more than 10, 9, 8, 7, 6, 5, 4, 3, or 2 amino acid substitutions. In some embodiments, the substitutions are conservative substitutions. In some embodiments, the substitutions are non-conservative. In some embodiments, the substitutions are a combination of conservative and non-conservative substitutions. In some embodiments, the modification in sequence is made at the binding site of the IgSF domain for its cognate binding partner.

In some embodiments, the wild-type or unmodified IgSF domain is a mammalian IgSF domain. In some embodiments, the wild-type or unmodified IgSF domain can be an IgSF domain that includes, but is not limited to, human, mouse, cynomolgus monkey, or rat. In some embodiments, the wild-type or unmodified IgSF domain is human.

In some embodiments, the wild-type or unmodified IgSF domain is an IgSF domain or specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NO:1-27 or a mature form thereof lacking the signal sequence, a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO:1-27 or a mature form thereof, or is a portion thereof containing an IgV domain or IgC domain or specific binding fragments thereof.

In some embodiments, the wild-type or unmodified IgSF domain is or comprises an extracellular domain of an IgSF family member or a portion thereof containing an IgSF domain (e.g. IgV domain or IgC domain). In some embodiments, the unmodified or wild-type IgSF domain comprises the amino acid sequence set forth in any of SEQ ID NOS:28-54, or an ortholog thereof. For example, the unmodified or wild-type IgSF domain can comprise (i) the sequence of amino acids set forth in any of SEQ ID NOS:28-54, (ii) a sequence of amino acids that has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to any of SEQ ID NOS: 28-54, or (iii) is a specific binding fragment of the sequence of amino acids set forth in any of SEQ ID NOS: 28-54 or a specific binding fragment of a sequence of amino acids that has at least at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to any of SEQ ID NOS: 28-54 comprising an IgV domain or an IgC domain.

In some embodiments, the extracellular domain of an unmodified or wild-type IgSF domain can comprise more than one IgSF domain, for example, an IgV domain and an IgC domain. However, the affinity modified IgSF domain need not comprise both the IgV domain and the IgC domain. In some embodiments, the affinity modified IgSF domain comprises or consists essentially of the IgV domain or a specific binding fragment thereof. In some embodiments, the affinity modified IgSF domain comprises or consists essentially of the IgC domain or a specific binding fragment thereof. In some embodiments, the affinity modified IgSF domain comprises the IgV domain or a specific binding fragment thereof, and the IgC domain or a specific binding fragment thereof.

In some embodiments, the one or more amino acid substitutions of the affinity modified IgSF domain can be located in any one or more of the IgSF polypeptide domains. For example, in some embodiments, one or more amino acid substitutions are located in the extracellular domain of the IgSF polypeptide. In some embodiments, one or more amino acid substitutions are located in the IgV domain or specific binding fragment of the IgV domain. In some embodiments, one or more amino acid substitutions are located in the IgC domain or specific binding fragment of the IgC domain.

In some embodiments, at least one IgSF domain, such as a mammalian IgSF domain, of an immunomodulatory protein provided herein is independently affinity modified in sequence to have at least 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86% 85%, or 80% sequence identity with a wild-type or unmodified IgSF domain or specific binding fragment thereof contained in a wild-type or unmodified IgSF protein, such as but not limited to, those disclosed in Table 1 as SEQ ID NOS: 1-27.

In some embodiments, the IgSF domain of an immunomodulatory protein provided herein is a specific binding fragment of a wild-type or unmodified IgSF domain contained in a wild-type or unmodified IgSF protein, such as but not limited to, those disclosed in Table 1 in SEQ ID NOS: 1-27. In some embodiments, the specific binding fragment can have an amino acid length of at least 50 amino acids, such as at least 60, 70, 80, 90, 100, or 110 amino acids. In some embodiments, the specific binding fragment of the IgV domain contains an amino acid sequence that is at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% of the length of the wild-type or unmodified IgV domain. In some embodiments, the specific binding fragment of the IgC domain comprises an amino acid sequence that is at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% of the length of the wild-type or unmodified IgC domain. In some embodiments, the specific binding fragment modulates immunological activity. In more specific embodiments, the specific binding fragment of an IgSF domain increases immunological activity. In alternative embodiments, the specific binding fragment decreases immunological activity.

To determine the percent identity of two nucleic acid sequences or of two amino acids, the sequences are aligned for optimal comparison purposes (e.g., gaps may be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=# of identical positions/total # of positions (e.g., overlapping positions)×100). In one embodiment the two sequences are the same length. One may manually align the sequences and count the number of identical nucleic acids or amino acids. Alternatively, alignment of two sequences for the determination of percent identity may be accomplished using a mathematical algorithm. Such an algorithm is incorporated into the NBLAST and XBLAST programs. BLAST nucleotide searches may be performed with the NBLAST program, score=100, wordlength=12, to obtain nucleotide sequences homologous to a nucleic acid molecules of the invention. BLAST protein searches may be performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to a protein molecule of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST may be utilized. Alternatively, PSI-Blast may be used to perform an iterated search which detects distant relationships between molecules. When utilising the NBLAST, XBLAST, and Gapped BLAST programs, the default parameters of the respective programs may be used such as those available on the NCBI website. Alternatively, sequence identity may be calculated after the sequences have been aligned e.g. by the BLAST program in the NCBI database. Generally, the default settings with respect to e.g. “scoring matrix” and “gap penalty” may be used for alignment. In the context of the present invention, the BLASTN and PSI BLAST NCBI default settings may be employed.

In some embodiments, the immunomodulatory protein contains at least one affinity modified IgSF domain. In some embodiments, the immunomodulatory protein further contains at least one affinity modified domain and further contains at least one non-affinity modified IgSF domain (e.g. unmodified or wildtype IgSF domain). In some embodiments, the immunomodulatory protein contains at least two affinity modified domains. In some embodiments, the immunomodulatory protein can contain a plurality of non-affinity modified IgSF domains and/or affinity modified IgSF domains such as 1, 2, 3, 4, 5, or 6 non-affinity modified IgSF and/or affinity modified IgSF domains.

In some embodiments, at least one non-affinity modified IgSF domain and/or one affinity modified IgSF domain present in an immunomodulatory protein provided herein specifically binds to at least one cell surface molecular species expressed on mammalian cells forming the immunological synapse (IS). Of course, in some embodiments, an immunomodulatory protein provided herein comprises a plurality of non-affinity modified IgSF domains and/or affinity modified IgSF domains such as 1, 2, 3, 4, 5, or 6 non-affinity modified IgSF and/or affinity modified IgSF domains. One or more of these non-affinity modified IgSF domains and/or affinity modified IgSF domains can independently specifically bind to either one or both of the mammalian cells forming the IS.

Often, the cell surface molecular species to which the affinity modified IgSF domain specifically binds will be the cognate binding partner of the wild type IgSF family member or wild type IgSF domain that has been affinity modified. In some embodiments, the cell surface molecular species is a mammalian IgSF member. In some embodiments, the cell surface molecular species is a human IgSF member. In some embodiments, the cell surface molecular species will be the cell surface cognate binding partners as indicated in Table 1. In some embodiments, the cell surface molecular species will be a viral protein, such as a poliovirus protein, on the cell surface of a mammalian cell such as a human cell.

In some embodiments, at least one non-affinity modified and/or affinity modified IgSF domain of an immunomodulatory protein provided herein binds to at least two or three cell surface molecular species present on mammalian cells forming the IS. The cell surface molecular species to which the non-affinity modified IgSF domains and/or the affinity modified IgSF domains of the invention specifically bind to can exclusively be on one or the other of the two mammalian cells (i.e. in cis configuration) forming the IS or, alternatively, the cell surface molecular species can be present on both.

In some embodiments, the affinity modified IgSF domain specifically binds to at least two cell surface molecular species wherein one of the molecular species is present on one of the two mammalian cells forming the IS and the other molecular species is present on the second of the two mammalian cells forming the IS. In such embodiments, the cell surface molecular species is not necessarily present solely on one or the other of the two mammalian cells forming the IS (i.e., in a trans configuration) although in some embodiments it is. Thus, embodiments provided herein include those wherein each cell surface molecular species is exclusively on one or the other of the mammalian cells forming the IS (cis configuration) as well as those where the cell surface molecular species to which each affinity modified IgSF binds is present on both of the mammalian cells forming the IS (i.e., cis and trans configuration).

Those of skill will recognize that antigen presenting cells (APCs) and tumor cells form an immunological synapse with lymphocytes. Thus, in some embodiments at least one non-affinity modified IgSF domain and/or at least one affinity modified IgSF domain of the immunomodulatory protein specifically binds to only cell surface molecular species present on a cancer cell, wherein the cancer cell in conjunction with a lymphocyte forms the IS. In other embodiments, at least one non-affinity modified IgSF domain and/or at least one affinity modified IgSF domain of the immunomodulatory protein specifically binds to only cell surface molecular species present on a lymphocyte, wherein the lymphocyte in conjunction with an APC or tumor cell forms the IS. In some embodiments, the non-affinity modified IgSF domain and/or affinity modified IgSF domain bind to cell surface molecular species present on both the target cell (or APC) and the lymphocyte forming the IS.

Embodiments of the invention include those in which an immunomodulatory protein provided herein comprises at least one affinity modified IgSF domain with an amino acid sequence that differs from a wild-type or unmodified IgSF domain (e.g. a mammalian IgSF domain) such that its binding affinity (or avidity if in a multimeric or other relevant structure), under specific binding conditions, to at least one of its cognate binding partners is either increased or decreased relative to the unaltered wild-type or unmodified IgSF domain control. In some embodiments, an affinity modified IgSF domain has a binding affinity for a cognate binding partner that differs from that of a wild-type or unmodified IgSF control sequence as determined by, for example, solid-phase ELISA immunoassays, flow cytometry or Biacore assays. In some embodiments, the IgSF domain has an increased binding affinity for one or more cognate binding partners. In some embodiments, the affinity modified IgSF domain has a decreased binding affinity for one or more cognate binding partners, relative to a wild-type or unmodified IgSF domain. In some embodiments, the cognate binding partner can be a mammalian protein, such as a human protein or a murine protein.

Binding affinities for each of the cognate binding partners are independent; that is, in some embodiments, an affinity modified IgSF domain has an increased binding affinity for one, two or three different cognate binding parters, and a decreased binding affinity for one, two or three of different cognate binding partners, relative to a wild-type or unmodified ICOSL polypeptide.

In some embodiments of an immunomodulatory protein provided herein, the binding affinity or avidity of the affinity modified IgSF domain is increased at least 10%, 20%, 30%, 40%, 50%, 100%, 200%, 300%, 400%, 500%, 1000%, 5000%, or 10,000% relative to the wild type or unmodified control IgSF domain. In some embodiments, the increase in binding affinity relative to the wild-type or unmodified IgSF domain is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold or 50-fold.

In some embodiments, the binding affinity or avidity is decreased at least 10%, and up to 20%, 30%, 40%, 50%, 60%, 70%, 80% or up to 90% relative to the wild type or unmodified control IgSF domain. In some embodiments, the decrease in binding affinity relative to the wild-type or unmodified IgSF domain is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold or 50-fold.

In some embodiments, the specific binding affinity of an affinity modified IgSF domain to a cognate binding partner can be at least 1×10⁻⁵ M, 1×10⁻⁶ M, 1×10⁻⁷ M, 1×10⁻⁸ M, 1×10⁻⁹ M, 1×10⁻¹⁰ M or 1×10⁻¹¹M, or 1×10⁻¹² M.

In some embodiments, an immunomodulatory protein provided comprises at least two IgSF domains in which at least one of the IgSF domain is affinity modified while in some embodiments both are affinity modified, and wherein at least one of the affinity modified IgSF domains has increased affinity (or avidity) to its cognate binding partner and at least one affinity modified IgSF domain has a decreased affinity (or avidity) to its cognate binding partner.

In some embodiments, an IgSF domain that otherwise binds to multiple cell surface molecular species is affinity modified such that it substantially no longer specifically binds to one of its cognate cell surface molecular species. Thus, in these embodiments the specific binding to one of its cognate cell surface molecular species is reduced to specific binding of no more than 10% of the wild type level and often no more than 7%, 5%, 3%, 1%, or no detectable or statistically significant specific binding.

In these embodiments, a specific binding site on a mammalian IgSF domain is inactivated or substantially inactivated with respect to at least one of the cell surface molecular species. Thus, for example, if a wild type IgSF domain specifically binds to exactly two cell surface molecular species then in some embodiments it is affinity modified to specifically bind to exactly one cell surface molecular species (whereby determination of the number of affinity modified IgSF domains disregards any substantially immunologically inactive fractional sequence thereof). And, if a wild type IgSF domain specifically binds to exactly three cell surface molecular species then in some embodiments it is affinity modified to specifically bind to exactly two cell surface molecular species. The IgSF domain that is affinity modified to substantially no longer specifically bind to one of its cognate cell surface molecular species can be an IgSF domain that otherwise specifically binds competitively or non-competitively to its cell surface molecular species. Those of skill will appreciate that a wild type IgSF domain that competitively binds to two cognate binding partners can nonetheless be inactivated with respect to exactly one of them if, for example, their binding sites are not not precisely coextensive but merely overlap such that specific binding of one inhibits binding of the other cognate binding partner and yet both competitive binding sites are distinct.

The non-affinity modified IgSF domains and/or affinity modified IgSF domains of the immunomodulatory proteins provided can in some embodiments specifically bind competitively to its cognate cell surface molecular species. In other embodiments the non-affinity modified IgSF domains and/or affinity modified IgSF domains of an immunomodulatory protein provided herein specifically bind non-competitively to its cognate cell surface molecular species. Any number of the non-affinity modified IgSF domains and/or affinity modified IgSF domains present in an immunomodulatory protein provided herein can specifically bind competitively or non-competitively.

In some embodiments, the immunomodulatory protein provided herein comprises at least two non-affinity modified IgSF domains, or at least one non-affinity modified IgSF domain and at least one affinity modified IgSF domain, or at least two affinity modified IgSF domains wherein one IgSF domain specifically binds competitively and a second IgSF domain binds non-competitively to its cognate cell surface molecular species. More generally, an immunomodulatory protein provided herein can comprise 1, 2, 3, 4, 5, or 6 competitive or 1, 2, 3, 4, 5, or 6 non-competitive binding non-affinity modified IgSF and/or affinity modified IgSF domains or any combination thereof. Thus, an immunomodulatory protein provided herein can have the number of non-competitive and competitive binding IgSF domains, respectively, of: 0 and 1, 0 and 2, 0 and 3, 0 and 4, 1 and 0, 1 and 1, 1 and 2, 1 and 3, 2 and 0, 2 and 1, 2 and 2, 2 and 3, 3 and 0, 3 and 1, 3 and 2, 3 and 3, 4 and 0, 4 and 1, and, 4 and 2.

A plurality of non-affinity modified and/or affinity modified IgSF domains immunomodulatory protein provided herein need not be covalently linked directly to one another. In some embodiments, an intervening span of one or more amino acid residues indirectly covalently bonds the non-affinity modified and/or affinity modified IgSF domains to each other. The linkage can be via the N-terminal to C-terminal residues.

In some embodiments, the linkage can be made via side chains of amino acid residues that are not located at the N-terminus or C-terminus of the non-affinity modified or affinity modified IgSF domain. Thus, linkages can be made via terminal or internal amino acid residues or combinations thereof.

The “peptide linkers” that link the non-affinity modified and/or affinity modified IgSF domains can be a single amino acid residue or greater in length. In some embodiments, the peptide linker has at least one amino acid residue but is no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid residues in length. In some embodiments, the linker is (in one-letter amino acid code): GGGGS (“4GS”) or multimers of the 4GS linker, such as repeats of 2, 3, 4, or 5 4GS linkers. In further optional embodiments, a series of alanine residues are interposed between 4GS linkers and to an Fc to which the immunomodulatory protein is covalently linked. In some embodiments, the number of alanine residues in each series is: 2, 3, 4, 5, or 6 alanines.

A. Exemplary Affinity Modified IgSF Domains

In some embodiments, the affinity modified IgSF domain has one or more amino acid substitutions in an IgSF domain of a wild-type or unmodified IgSF protein, such as set forth in Table 1 above. The one or more amino acid substitutions can be in the ectodomain of the wild-type or unmodified IgSF domain, such as the extracellular domain. In some embodiments, the one or more amino acid substitutions are in the IgV domain or specific binding fragment thereof. In some embodiments, the one or more amino acid substitutions are in the IgC domain or specific binding fragment thereof. In some embodiments of the affinity modified IgSF domain, some of the one or more amino acid substitutions are in the IgV domain or a specific binding fragment thereof, and some of the one or more amino acid substitutions are in the IgC domain or a specific binding fragment thereof.

In some embodiments, the affinity modified IgSF domain has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid substitutions. The substitutions can be in the IgV domain or the IgC domain. In some embodiments, the affinity modified IgSF domain has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid substitutions in the IgV domain or specific binding fragment thereof. In some embodiments, the affinity modified IgSF domain has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid substitutions in the IgC domain or specific binding fragment thereof. In some embodiments, the affinity modified IgSF domain has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the wild-type or unmodified IgSF domain or specific binding fragment thereof, such as the IgSF domain contained in the IgSF protein set forth in any of SEQ ID NOS: 1-27.

In some embodiments, the affinity modified IgSF domain contains one or more amino acid substitutions in a wild-type or unmodified IgSF domain of a B7 IgSF family member. In some embodiments, the B7 IgSF family member is CD80, CD86 or ICOS Ligand (ICOSL). In some embodiments, the affinity modified IgSF domain has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the wild-type or unmodified IgSF domain or specific binding fragment thereof, such as the IgSF domain contained in the IgSF protein set forth in any of SEQ ID NOS: 1, 2 or 5. Exemplary affinity modified IgSF domains of CD80 are set forth in Table 2. Exemplary affinity modified IgSF domains of ICOSL are set forth in Table 3. Exemplary affinity modified IgSF domains of CD86 are set forth in Table 4.

TABLE 2 Exemplary variant CD80 polypeptides ECD IgV SEQ ID SEQ ID Mutation(s) NO NO Wild-type 28 152 L70Q/A91G 55 153 L70Q/A91G/T130A 56 L70Q/A91G/I118A/T120S/T130A 57 V4M/L70Q/A91G/T120S/T130A 58 154 L70Q/A91G/T120S/T130A 59 V20L/L70Q/A91S/T120S/T130A 60 155 S44P/L70Q/A91G/T130A 61 156 L70Q/A91G/E117G/T120S/T130A 62 A91G/T120S/T130A 63 157 L70R/A91G/T120S/T130A 64 158 L70Q/E81A/A91G/T120S/I127T/T130A 65 159 L70Q/Y87N/A91G/T130A 66 160 T28S/L70Q/A91G/E95K/T120S/T130A 67 161 N63S/L70Q/A91G/T120S/T130A 68 162 K36E/I67T/L70Q/A91G/T120S/T130A/N152T 69 163 E52G/L70Q/A91G/T120S/T130A 70 164 K37E/F59S/L70Q/A91G/T120S/T130A 71 165 A91G/S103P 72 K89E/T130A 73 166 A91G 74 D60V/A91G/T120S/T130A 75 167 K54M/A91G/T120S 76 168 M38T/L70Q/E77G/A91G/T120S/T130A/N152T 77 169 R29H/E52G/L70R/E88G/A91G/T130A 78 170 Y31H/T41G/L70Q/A91G/T120S/T130A 79 171 V68A/110A 80 172 S66H/D90G/T110A/F116L 81 173 R29H/E52G/T120S/T130A 82 174 A91G/L102S 83 I67T/L70Q/A91G/T120S 84 175 L70Q/A91G/T110A/T120S/T130A 85 M38V/T41D/M43I/W50G/D76G/V83A/K89E/ 86 176 T120S/T130A V22A/L70Q/S121P 87 177 A12V/S15F/Y31H/T41G/T130A/P137L/N152T 88 178 I67F/L70R/E88G/A91G/T120S/T130A 89 179 E24G/L25P/L70Q/T120S 90 180 A91G/F92L/F108L/T120S 91 181 R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/ 92 182 M47T/E81V/L85R/K89N/A91T/F92P/K93V/ R94L/I118T/N149S R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/ 93 M47T/E81V/L85R/K89N/A91T/F92P/K93V/ R94L/N144S/N149S R29D/Y31L/Q33H/K36G/M38I/T41A/M42T/ 94 183 M43R/M47T/E81V/L85R/K89N/A91T/F92P/ K93V/R94L/L148S/N149S E24G/R29D/Y31L/Q33H/K36G/M38I/T41A/ 95 184 M43R/M47T/F59L/E81V/L85R/K89N/A91T/ F92P/K93V/R94L/H96R/N149S/C182S R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/ 96 M47T/E81V/L85R/K89N/A91T/F92P/ K93V/R94L/N149S R29V/M43Q/E81R/L85I/K89R/D90L/ 97 185 A91E/F92N/K93Q/R94G T41I/A91G 98 186 K89R/D90K/A91G/F92Y/K93R/N122S/N177S 99 187 K89R/D90K/A91G/F92Y/K93R 100 K36G/K37Q/M38I/F59L/E81V/L85R/ 101 188 K89N/A91T/F92P/K93V/R94L/E99G/ T130A/N149S E88D/K89R/D90K/A91G/F92Y/K93R 102 189 K36G/K37Q/M38I/L40M 103 190 K36G 104 191 R29H/Y31H/T41G/Y87N/E88G/K89E/ 105 192 D90N/A91G/P109S A12T/H18L/N43V/F59L/E77K/P109S/I118T 106 193 R29V/Y31F/K36G/M38L/N43Q/E81R/V83I/ 107 194 L85I/K89R/D90L/A91E/F92N/K93Q/R94G V68M/L70P/L72P/K86E 108 195

TABLE 3 Exemplary variant ICOSL polypeptides ECD IgV SEQ ID SEQ ID Mutation(s) NO NO Wild-type 32 196 N52S 109 197 N52H 110 198 N52D 111 199 N52Y/N57Y/F138L/L203P 112 200 N52H/N57Y/Q100P 113 201 N52S/Y146C/Y152C 114 N52H/C198R 115 N52H/C140D/T225A 116 N52H/C198R/T225A 117 N52H/K92R 118 202 N52H/S99G 119 203 N52Y 120 204 N57Y 121 205 N57Y/Q100P 122 206 N52S/S130G/Y152C 123 N52S/Y152C 124 N52S/C198R 125 N52Y/N57Y/Y152C 126 N52Y/N57Y/129P/C198R 127 N52H/L161P/C198R 128 N52S/T113E 129 S54A 130 207 N52D/S54P 131 208 N52K/L208P 132 209 N52S/Y152H 133 N52D/V151A 134 N52H/I143T 135 N52S/L80P 136 210 F120S/Y152H/N201S 137 N52S/R75Q/L203P 138 211 N52S/D158G 139 N52D/Q133H 140 N52S/N57Y/H94D/L96F/L98F/Q100R 141 212 N52S/N57Y/H94D/L96F/L98F/Q100R/G103E/F120S 142 213 N52S/G103E 239 240

TABLE 4 Exemplary variant CD86 polypeptides ECD IgC SEQ ID SEQ ID Mutation(s) NO NO Wild-type 29 220 Q35H/H90L/Q102H 148 221 Q35H 149 222 H90L 150 223 Q102H 151 224

In some embodiments, the affinity modified IgSF domain contains one or more amino acid substitutions in a wild-type or unmodified IgSF domain of an NkP30 family member. In some embodiments, the affinity modified IgSF domain has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the wild-type or unmodified IgSF domain or specific binding fragment thereof, such as the IgSF domain contained in the IgSF protein set forth in SEQ ID NO:27. Table 5 provides exemplary affinity modified NkP30 IgSF domains.

TABLE 5 Exemplary variant NKp30 polypeptides ECD IgV SEQ ID SEQ ID Mutation(s) NO NO Wild-type 54 214 L30V/A60V/S64P/S86G 143 215 L30V 144 216 A60V 145 217 S64P 146 218 S86G 147 219

B. Types of Affinity-Modified Immunomodulatory Protein

1. Dual Binding Affinity Modified Domain

In some embodiments, the immunomodulatory protein provided herein can comprise the sequence of at least one IgSF domain of a wild-type mammalian non-immunoglobulin (i.e., non-antibody) IgSF family member, wherein at least one IgSF domain therein is affinity modified (“Type I” immunomodulatory proteins). In some embodiments, the at least one modified IgSF domain specifically binds non-competitively to the at least two cognate binding partners.

In some embodiments, the immunomodulatory protein comprises at least one non-immunoglobulin affinity modified immunoglobulin superfamily (IgSF) domain that specifically binds non-competitively to at least two cognate binding partners. In some embodiments, the affinity modified domain exhibits increased binding to at least one of the cognate binding partners compared to the wild-type or unmodified IgSF domain. In some embodiments, the affinity modified domain exhibits increased binding to at least two different cognate binding partners.

In some embodiments of a Type I immunomodulatory protein of the invention, the unmodified or wild-type IgSF member, such as mammalian IgSF member, is one of the IgSF members or comprise an IgSF domain from one of the IgSF members as indicated in Table 1 including any mammalian orthologs thereof.

In some embodiments, additional IgSF domains present within the Type I immunomodulatory protein can be non-affinity modified and/or affinity modified, such as at least two, three, four, or five IgSF domains and, in some embodiments, exactly two, three, four, or five IgSF domains.

In some embodiments, a Type I immunomodulatory protein herein comprising at least one non-immunoglobulin affinity modified immunoglobulin superfamily (IgSF) domain comprising one or more amino acid substitution(s) in a wild-type or unmodified IgSF domain, in which the affinity modified IgSF domain has 1) altered, e.g. increased or decreased, binding to at least two cognate binding partners compared to the wild-type or unmodified IgSF domain; and 2) the at least one affinity modified IgSF domain specifically binds non-competitively to the at least two cognate binding partners. In some embodiments, the affinity modified IgSF domain of the Type I immunomodulatory protein has increased binding to at least two cognate binding partners. In some embodiments, the affinity modified IgSF domain of the Type I immunomodulatory protein has decreased binding to at least two cognate binding partners. In some embodiments, the affinity modified IgSF domain of the Type I immunomodulatory protein has increased binding to at least one cognate binding partner and decreased binding to at least one other different cognate binding partner.

In some embodiments, the two cognate binding partners are expressed on the surface of at least two different cells, such as two different mammalian cells. For example, in some embodiments, one cognate binding partner is expressed on a lymphocyte and another cognate binding partner is expressed on an antigen-presenting cells. In some embodiments, the two cognate binding partners are expressed on the same cell type, such as same immune cell. In some embodiment, the Type I immunomodulatory protein is capable of modulating the immunological activity of one or more of the immune cells, such as the immunological activity of a lymphocyte, for example, a T cell. In some embodiments, immunological activity is increased. In some embodiments, immunological activity is decreased.

In some embodiments, the immunomodulatory protein comprises or consists essentially of only one affinity modified IgSF domain, which binds non-competitively to the at least two cognate binding partners. In some embodiments, the affinity modified domain is an affinity modified IgV domain. In some embodiments, the affinity modified domain is an affinity modified IgC domain.

In some embodiments, a Type I immunomodulatory protein provided herein comprises an affinity modified CD80 IgSF domain that non-competitively specifically binds to CD28 and PDL1. In some embodiments, the affinity modified CD80 IgSF domain is an IgV domain. In some embodiments, the immunomodulatory protein further comprises a further non-affinity modified IgSF domain.

2. Stacked or Multi-Domain Immunomodulatory Proteins

In some embodiments of the present invention, an immunomodulatory protein comprises a combination (a “non-wild-type combination”) and/or arrangement (a “non-wild type arrangement” or “non-wild-type permutation”) of an affinity modified and/or non-affinity modified IgSF domain sequences that are not found in wild-type IgSF family members (“Type II” immunomodulatory proteins). The sequences of the IgSF domains which are non-affinity modified (e.g., wild-type) or have been affinity modified can be mammalian, such as from mouse, rat, cynomolgus monkey, or human origin, or combinations thereof. The number of such non-affinity modified or affinity modified IgSF domains present in these embodiments of a Type II immunomodulatory protein (whether non-wild type combinations or non-wild type arrangements) is at least 2, 3, 4, or 5 and in some embodiments exactly 2, 3, 4, or 5 IgSF domains (whereby determination of the number of affinity modified IgSF domains disregards any non-specific binding fractional sequences thereof and/or substantially immunologically inactive fractional sequences thereof).

In some embodiments, the Type II immunomodulatory proteins of the invention comprise a non-wild type combination of IgSF domains wherein the IgSF domains can be an IgSF domain of an IgSF family member from those listed in Table 1. Thus, in some embodiments, the immunodulatory protein can contain a first and second IgSF domain that can each be an affinity-modified IgSF domain containing one or more amino acid substitutions compared to an IgSF domain contained in an IgSF family member set forth in Table 1.

In some embodiments, IgSF domains are each independently an affinity or non-affinity modified IgSF domain contained in an IgSF family member of a family selected from Signal-Regulatory Protein (SIRP) Family, Triggering Receptor Expressed On Myeloid Cells Like (TREML) Family, Carcinoembryonic Antigen-related Cell Adhesion Molecule (CEACAM) Family, Sialic Acid Binding Ig-Like Lectin (SIGLEC) Family, Butyrophilin Family, B7 family, CD28 family, V-set and Immunoglobulin Domain Containing (VSIG) family, V-set transmembrane Domain (VSTM) family, Major Histocompatibility Complex (MHC) family, Signaling lymphocytic activation molecule (SLAM) family, Leukocyte immunoglobulin-like receptor (LIR), Nectin (Nec) family, Nectin-like (NECL) family, Poliovirus receptor related (PVR) family, Natural cytotoxicity triggering receptor (NCR) family, T cell immunoglobulin and mucin (TIM) family or Killer-cell immunoglobulin-like receptors (KIR) family. In some embodiments, the IgSF domains are each independently derived from an IgSF protein selected from the group consisting of CD80(B7-1), CD86(B7-2), CD274 (PD-L1, B7-H1), PDCD1LG2(PD-L2, CD273), ICOSLG(B7RP1, CD275, ICOSL, B7-H2), CD276(B7-H3), VTCN1(B7-H4), CD28, CTLA4, PDCD1(PD-1), ICOS, BTLA(CD272), CD4, CD8A(CD8-alpha), CD8B(CD8-beta), LAG3, HAVCR2(TIM-3), CEACAM1, TIGIT, PVR(CD155), PVRL2(CD112), CD226, CD2, CD160, CD200, CD200R1(CD200R), and NC R3 (NKp30).

In some embodiments, the IgSF domains independently contain one or more amino acid substitutions compared to an IgSF domain in a wild-type or unmodified IgSF domain, such as an IgSF domain in an IgSF family member set forth in Table 1. In some embodiments, the affinity-modified IgSF domain comprises at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to a wild-type or unmodified IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27. In some embodiments, the wild-type or unmodified IgSF domain is an IgV domain or an IgC domain, such as an IgC1 or IgC2 domain. In some embodiments, the affinity modified IgSF domain is an affinity-modified IgV domain or IgC domain.

In some embodiments of a Type II immunomodulatory protein of the invention, the number of IgSF domains is at least 2 wherein the number of affinity modified and the number of non-affinity modified IgSF domains is each independently at least: 0, 1, 2, 3, 4, 5, or 6. Thus, the number of affinity modified IgSF domains and the number of non-affinity modified IgSF domains, respectively, (affinity modified IgSF domain: non-affinity modified IgSF domain), can be exactly or at least: 2:0 (affinity modified: wild-type), 0:2, 2:1, 1:2, 2:2, 2:3, 3:2, 2:4, 4:2, 1:1, 1:3, 3:1, 1:4, 4:1, 1:5, or 5:1.

In some embodiments of a Type II immunomodulatory protein, at least two of the non-affinity modified and/or affinity modified IgSF domains are identical IgSF domains.

In some embodiments, a Type II immunomodulatory protein of the present invention comprises at least two affinity modified and/or non-affinity modified IgSF domains from a single IgSF member but in a non-wild-type arrangement (alternatively, “permutation”). One illustrative example of a non-wild type arrangement or permutation is an immunomodulatory protein of the present invention comprising a non-wild-type order of affinity modified and/or non-affinity modified IgSF domain sequences relative to those found in the wild-type mammalian IgSF family member whose IgSF domain sequences served as the source of the non-affinity modified and/or affinity modified IgSF domains. The mammalian wild-type IgSF members in the preceding embodiment specifically includes those listed in Table 1. Thus, in one example, if the wild-type family member comprises an IgC1 domain proximal to the transmembrane domain of a cell surface protein and an IgV domain distal to the transmembrane domain, then an immunomodulatory protein of the present invention can comprise an IgV proximal and an IgC1 distal to the transmembrane domain albeit in a non-affinity modified and/or affinity modified form. The presence, in an immunomodulatory protein of the present invention, of both non-wild-type combinations and non-wild-type arrangements of non-affinity modified and/or affinity modified IgSF domains is also within the scope of the present invention.

In some embodiments of a Type II immunomodulatory protein, the non-affinity modified and/or affinity modified IgSF domains are non-identical (i.e., different) IgSF domains. Non-identical affinity modified IgSF domains specifically bind, under specific binding conditions, different cognate binding partners and are “non-identical” irrespective of whether or not the wild-type IgSF domains from which they are engineered was the same. Thus, for example, a non-wild-type combination of at least two non-identical IgSF domains in an immunomodulatory protein of the present invention can comprise at least one IgSF domain sequence whose origin is from and unique to one IgSF family member, and at least one of a second IgSF domain sequence whose origin is from and unique to another IgSF family member, wherein the IgSF domains of the immunomodulatory protein are in non-affinity modified and/or affinity modified form. However, in alternative embodiments, the two non-identical IgSF domains originate from the same IgSF domain sequence but at least one is affinity modified such that they specifically bind to different cognate binding partners.

In some embodiments, the number of non-identical non-affinity modified and/or affinity modified IgSF domains present in an immunomodulatory protein of the invention is at least 2, 3, 4, or 5 and in some embodiments exactly 2, 3, 4, or 5 non-identical non-affinity modified and/or affinity modified IgSF domains. In some embodiments, the non-identical IgSF domains are combinations from at least two IgSF members indicated in Table 1, and in some embodiments at least 3 or 4 IgSF members of Table 1.

In some specific embodiments, a Type II immunomodulatory protein of the invention comprises an affinity modified NKp30 IgSF domain and an affinity modified ICOSLG IgSF domain, affinity modified CD80 IgSF domain or an affinity modified CD86 IgSF domain. In some embodiments, a Type II immunomodulatory protein comprises an affinity modified IgSF domain from at least two B7 family members. In some embodiments, the immunomodulatory proteins comprises at least two affinity modified domains from an affinity modified CD80 IgSF domain, an affinity modified ICOSL IgSF domain or an affinity modified CD86 IgSF domain or specific binding fragments thereof. In some embodiments, the affinity modified domains are linked via at least or exactly 1, 2, 3, 4 G4S domains.

A plurality of non-affinity modified and/or affinity modified IgSF domains in a stacked immunomodulatory protein polypeptide chain need not be covalently linked directly to one another. In some embodiments, an intervening span of one or more amino acid residues indirectly covalently bonds the non-affinity modified and/or affinity modified IgSF domains to each other. The linkage can be via the N-terminal to C-terminal residues.

In some embodiments, the linkage can be made via side chains of amino acid residues that are not located at the N-terminus or C-terminus of the non-affinity modified and/or affinity modified IgSF domain. Thus, linkages can be made via terminal or internal amino acid residues or combinations thereof.

In some embodiments, the “peptide linkers” that link the non-affinity modified and/or affinity modified IgSF domains can be a single amino acid residue or greater in length. In some embodiments, the peptide linker has at least one amino acid residue but is no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid residues in length. In some embodiments, the linker is (in one-letter amino acid code): GGGGS (“4GS”) or multimers of the 4GS linker, such as repeats of 2, 3, 4, or 5 4GS linkers. In further optional embodiments, a series of alanine residues are interposed between a peptide linker (such as a 4GS linker or multimer thereof) and an Fc to which the immunomodulatory protein is covalently linked. In some embodiments, the number of alanine residues in each series is: 2, 3, 4, 5, or 6 alanines.

In some embodiments, the non-affinity modified and/or affinity modified IgSF domains are linked by “wild-type peptide linkers” inserted at the N-terminus and/or C-terminus of the first and/or second non-affinity modified and/or affinity modified IgSF domains. In some embodiments, there is present a leading peptide linker inserted at the N-terminus of the first IgSF domain and/or a first trailing sequence inserted at the C-terminus of the first non-affinity modified and/or affinity modified IgSF domain. In some embodiments, there is present a second leading peptide linker inserted at the N-terminus of the second IgSF domain and/or a second trailing sequence inserted at the C-terminus of the second non-affinity modified and/or affinity modified IgSF domain. When the first and second non-affinity modified and/or affinity modified IgSF domains are derived from the same parental protein and are connected in the same orientation, wild-type peptide linkers between the first and second non-affinity modified and/or affinity modified IgSF domains are not duplicated. For example, when the first trailing wild-type peptide linker and the second leading wild-type peptide linker are the same, the Type II immunomodulatory protein does not comprise either the first trailing wild-type peptide linker or the second leading wild-type peptide linker.

In some embodiments, the Type II immunomodulatory protein comprises a first leading wild-type peptide linker inserted at the N-terminus of the first non-affinity modified and/or affinity modified IgSF domain, wherein the first leading wild-type peptide linker comprises at least 5 (such as at least about any of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more) consecutive amino acids from the intervening sequence in the wild-type protein from which the first non-affinity modified and/or affinity modified IgSF domain is derived between the parental IgSF domain and the immediately preceding domain (such as a signal peptide or an IgSF domain). In some embodiments, the first leading wild-type peptide linker comprises the entire intervening sequence in the wild-type protein from which the first non-affinity modified and/or affinity modified IgSF domain is derived between the parental IgSF domain and the immediately preceding domain (such as a signal peptide or an IgSF domain).

In some embodiments, the Type II immunomodulatory protein further comprises a first trailing wild-type peptide linker inserted at the C-terminus of the first non-affinity modified and/or affinity modified IgSF domain, wherein the first trailing wild-type peptide linker comprises at least 5 (such as at least about any of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more) consecutive amino acids from the intervening sequence in the wild-type protein from which the first non-affinity modified and/or affinity modified IgSF domain is derived between the parental IgSF domain and the immediately following domain (such as an IgSF domain or a transmembrane domain). In some embodiments, the first trailing wild-type peptide linker comprises the entire intervening sequence in the wild-type protein from which the first non-affinity modified and/or affinity modified IgSF domain is derived between the parental IgSF domain and the immediately following domain (such as an IgSF domain or a transmembrane domain).

In some embodiments, the Type II immunomodulatory protein further comprises a second leading wild-type peptide linker inserted at the N-terminus of the second non-affinity modified and/or affinity modified IgSF domain, wherein the second leading wild-type peptide linker comprises at least 5 (such as at least about any of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more) consecutive amino acids from the intervening sequence in the wild-type protein from which the second non-affinity modified and/or affinity modified IgSF domain is derived between the parental IgSF domain and the immediately preceding domain (such as a signal peptide or an IgSF domain). In some embodiments, the second leading wild-type peptide linker comprises the entire intervening sequence in the wild-type protein from which the second non-affinity modified and/or affinity modified IgSF domain is derived between the parental IgSF domain and the immediately preceding domain (such as a signal peptide or an IgSF domain).

In some embodiments, the Type II immunomodulatory protein further comprises a second trailing wild-type peptide linker inserted at the C-terminus of the second non-affinity modified and/or affinity modified IgSF domain, wherein the second trailing wild-type peptide linker comprises at least 5 (such as at least about any of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more) consecutive amino acids from the intervening sequence in the wild-type protein from which the second non-affinity modified and/or affinity modified IgSF domain is derived between the parental IgSF domain and the immediately following domain (such as an IgSF domain or a transmembrane domain). In some embodiments, the second trailing wild-type peptide linker comprises the entire intervening sequence in the wild-type protein from which the second non-affinity modified and/or affinity modified IgSF domain is derived between the parental IgSF domain and the immediately following domain (such as an IgSF domain or a transmembrane domain).

Exemplary of a leading sequence and trailing sequence for a Type II protein containing a CD80 IgSF domain is set forth in SEQ ID NO:231 and SEQ ID NO:232. Exemplary of a leading sequence and trailing sequence for a Type II protein containing an ICOSL IgSF domain is set forth in SEQ ID NO: 233 and 234. Exemplary of a leading sequence and a trailing sequence for a Type II protein containing an CD86 IgSF domain is set forth in any of SEQ ID NOS: 236-238. Exemplary of a wild-type linker sequence for a Type II protein containing an NKp30 IgSF domain is set forth in SEQ ID NO:235.

C. Format of Affinity-Modified Immunomodulatory Protein

In some embodiments an immunomodulatory protein provided herein is in soluble form. Those of skill will appreciate that cell surface proteins typically have an intracellular, transmembrane, and extracellular domain (ECD) and that a soluble form of such proteins can be made using the extracellular domain or an immunologically active subsequence thereof. Thus, in some embodiments, the immunomodulatory protein containing an affinity modified IgSF domain lacks a transmembrane domain or a portion of the transmembrane domain. In some embodiments, the immunomodulatory protein containing an affinity modified IgSF domain lacks the intracellular (cytoplasmic) domain or a portion of the intracellular domain. In some embodiments, the immunomodulatory protein contains an affinity modified IgSF domain that only contains the ECD domain or a portion thereof containing an IgV domain and/or IgC domain or specific binding fragments thereof.

In some embodiments, the soluble form of an immunomodulatory protein of the present invention is covalently bonded, directly or indirectly, to an immunoglobulin Fc. Generally, the Fc is covalently bonded to the amino terminus of the immunomodulatory protein. The immunoglobulin Fc is in some embodiments a mammalian IgG class immunoglobulin, such as IgG1 or IgG2. In particular embodiments, the Fc will be human IgG1 or IgG2 Fc. It will be appreciated by those of skill in the art that small changes, such as 1, 2, 3, or 4, amino acid substitutions, deletions, additions, or combinations thereof, can be made to an Fc without substantially changing its pharmacokinetic properties. Such changes made be made, for example, to aid in manufacturability or to enhance, suppress, or eliminate antibody-dependent cell-mediated cytotoxicity. The term “Fc” as used herein is meant to embrace such molecules.

In some embodiments, the Fc is murine or human Fc. In some embodiments, the Fc is derived from IgG1, such as human IgG1. In some embodiments, the Fc comprises the amino acid sequence set forth in SEQ ID NO: 226 or a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO:226. In some embodiments, the Fc is derived from IgG2, such as human IgG2. In some embodiments, the Fc comprises the amino acid sequence set forth in SEQ ID NO: 227 or a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO:227.

In some embodiments, one or more amino acid modifications may be introduced into the Fc region of an IgSF-Fc variant fusion provided herein, thereby generating an Fc region variant. In some embodiments, the Fc region variant has decreased effector function. There are many examples of changes or mutations to Fc sequences that can alter effector function. For example, WO 00/42072, WO2006019447 and Shields et al. J Biol. Chem. 9(2): 6591-6604 (2001) describe exemplary Fc variants with improved or diminished binding to FcRs. The contents of those publications are specifically incorporated herein by reference.

In some embodiments, the Fc region that possesses some but not all effector functions, which makes it a desirable candidate for applications in which the half-life of the Fc fusion in vivo is important yet certain effector functions (such as CDC and ADCC) are unnecessary or deleterious. In vitro and/or in vivo cytotoxicity assays can be conducted to confirm the reduction/depletion of CDC and/or ADCC activities. For example, Fc receptor (FcR) binding assays can be conducted to ensure that the Fc-ICOSL variant fusion lacks FcγR binding (hence likely lacking ADCC activity), but retains FcRn binding ability. The primary cells for mediating ADCC, NK cells, express FcγRIII only, whereas monocytes express FcγRI, FcγRII and FcγRIII. FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol. 9:457-492 (1991). Non-limiting examples of in vitro assays to assess ADCC activity of a molecule of interest is described in U.S. Pat. No. 5,500,362 (see, e.g. Hellstrom, I. et al. Proc. Nat'l Acad. Sci. USA 83:7059-7063 (1986)) and Hellstrom, I et al., Proc. Nat'l Acad. Sci. USA 82:1499-1502 (1985); U.S. Pat. No. 5,821,337 (see Bruggemann, M. et al., J. Exp. Med. 166:1351-1361 (1987)). Alternatively, non-radioactive assay methods may be employed (see, for example, ACTI™ non-radioactive cytotoxicity assay for flow cytometry (CellTechnology, Inc. Mountain View, Calif.; and CytoTox 96™ non-radioactive cytotoxicity assay (Promega, Madison, Wis.). Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, e.g., in an animal model such as that disclosed in Clynes et al. Proc. Nat'l Acad. Sci. USA 95:652-656 (1998). C1q binding assays may also be carried out to confirm that the Fc-ICOSL variant fusion is unable to bind C1q and hence lacks CDC activity. See, e.g., C1q and C3c binding ELISA in WO 2006/029879 and WO 2005/100402. To assess complement activation, a CDC assay may be performed (see, for example, Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996); Cragg, M. S. et al., Blood 101:1045-1052 (2003); and Cragg, M. S. and M. J. Glennie, Blood 103:2738-2743 (2004)). FcRn binding and in vivo clearance/half life determinations can also be performed using methods known in the art (see, e.g., Petkova, S. B. et al., Int'l. Immunol. 18(12):1759-1769 (2006)).

Fc fusions with reduced effector function include those with substitution of one or more of Fc region residues 238, 265, 269, 270, 297, 327 and 329 by EU numbering (U.S. Pat. No. 6,737,056). Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327 by EU numbering, including the so-called “DANA” Fc mutant with substitution of residues 265 and 297 to alanine (U.S. Pat. No. 7,332,581).

Certain Fc variants with improved or diminished binding to FcRs are described. (See, e.g., U.S. Pat. No. 6,737,056; WO 2004/056312, WO2006019447 and Shields et al., J. Biol. Chem. 9(2): 6591-6604 (2001).)

In some embodiments, alterations are made in the Fc region that result in diminished C1q binding and/or Complement Dependent Cytotoxicity (CDC), e.g., as described in U.S. Pat. No. 6,194,551, WO 99/51642, and Idusogie et al., J. Immunol. 164: 4178-4184 (2000).

In some embodiments, there is provided an ICOSL-Fc variant fusion comprising a variant Fc region comprising one or more amino acid substitutions which increase half-life and/or improve binding to the neonatal Fc receptor (FcRn). Antibodies with increased half-lives and improved binding to FcRn are described in US2005/0014934A1 (Hinton et al.). Those antibodies comprise an Fc region with one or more substitutions therein which improve binding of the Fc region to FcRn. Such Fc variants include those with substitutions at one or more of Fc region residues: 238, 256, 265, 272, 286, 303, 305, 307, 311, 312, 317, 340, 356, 360, 362, 376, 378, 380, 382, 413, 424 or 434 by EU numbering, e.g., substitution of Fc region residue 434 (U.S. Pat. No. 7,371,826).

See also Duncan & Winter, Nature 322:738-40 (1988); U.S. Pat. No. 5,648,260; U.S. Pat. No. 5,624,821; and WO 94/29351 concerning other examples of Fc region variants.

In some embodiments, the Fc is an IgG1 variant that contains at least one amino acid substitution that is N82G by numbering of SEQ ID NO:226 (corresponding to N297G by EU numbering). In some embodiments, the variant Fc region further comprises a C5S amino acid modification. For example, in some embodiments, the variant Fc region comprises the following amino acid modifications: C5S and N82G.

In some embodiments, indirect covalent bonding of an Fc to an immunomodulatory protein of the present invention can be made via, for example, via a single amino acid or via a peptide (two or more amino acid residues in length) linker. Further, the single polypeptide chains of such Fc-fusion molecules can be dimerized through a variety of means including via inter-polypeptide chain disulfide bonds. Dimerized forms of the immunomodulatory proteins of the invention can comprise two identical or substantially identical species of polypeptides of the invention (homodimers), or separate species of polypeptide chains of the invention (heterodimers). It will be appreciated that microheterogeneities can exist even between the same species of polypeptide chain owing to minor differences in amino-terminus and carboxy-terminus residues from minor differences in expression or proteolysis, or to differences resulting from post-translational modification. Nonetheless, such substantially identical chains are deemed to be homodimeric. Derivatized immunomodulatory proteins are within the scope of the present invention and are often made to, for example, provide altered physico-chemical or pharmacokinetic properties.

In even more specific embodiments, the preceding specific embodiments are covalently linked to an Fc, such as a human IgG1 or IgG2 domain. In a further specific embodiment, the Fc is attached to an immunomodulatory protein via one or more G4S domains, often with at least or exactly one, two, three, four, or five successive alanine residues directly linked to the Fc and to the immunomodulatory protein.

In other embodiments, an immunomodulatory protein provided herein is bound to a liposomal membrane. A variety of methods to covalently or non-covalently attach proteins to a liposome surface are known in the art such as by amide conjugation or disulfide/thioether conjugation.

D. Functional Activity of Immunomodulatory Proteins

In some embodiments, the immunomodulatory proteins containing an affinity modified IgSF domain provided herein (full-length and/or specific binding fragments or stack constructs or fusion thereof) exhibit immunomodulatory activity to modulate T cell activation. Functionally, and irrespective of whether specific binding to its cognate binding partner is increased or decreased, the immunomodulatory proteins provided herein act to enhance or suppress immunological activity of lymphocytes relative to lymphocytes under the appropriate assay controls, such as in an MLR assay. In some embodiments, an immunomodulatory protein provided herein comprises at least two affinity modified IgSF domains wherein at least one of the affinity modified IgSF domains acts to enhance immunological activity and at least one affinity modified IgSF domain acts to suppress immunological activity.

In some embodiments, the provided immunomodulatory proteins modulate IFN-gamma expression in a primary T cell assay relative to a wild-type or unmodified IgSF domain control. In some cases, modulation of IFN-gamma expression can increase or decrease IFN-gamma expression relative to the control. Assays to determine specific binding and IFN-gamma expression are well-known in the art and include the MLR (mixed lymphocyte reaction) assays measuring interferon-gamma cytokine levels in culture supernatants (Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56), SEB (staphylococcal enterotoxin B) T cell stimulation assay (Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56), and anti-CD3 T cell stimulation assays (Li and Kurlander, J Transl Med. 2010: 8: 104).

In some embodiments, an immunomodulatory protein containing an affinity modified domain can in some embodiments increase or, in alternative embodiments, decrease IFN-gamma (interferon-gamma) expression in a primary T-cell assay relative to a wild-type IgSF domain control. In some embodiments of the provided polypeptides containing an affinity modified IgSF domain, the polypeptide can increase IFN-gamma expression and, in alternative embodiments, decrease IFN-gamma expression in a primary T-cell assay relative to a wild-type ICOSL control. In some embodiments of the provided polypeptides containing multiple affinity modified IgSF domains, the polypeptide can increase IFN-gamma expression and, in alternative embodiments, decrease IFN-gamma expression in a primary T-cell assay relative to a wild-type IgSF domain control.

Those of skill will recognize that the format of the primary T-cell assay used to determine an increase in IFN-gamma expression can differ from that employed to assay for a decrease in IFN-gamma expression. In assaying for the ability of an immunomodulatory protein to decrease IFN-gamma expression in a primary T-cell assay, a Mixed Lymphocyte Reaction (MLR) assay can be used as described in Example 6. In some cases, a soluble form of immunomodulatory protein can be employed to determine the ability of the affinity modified IgSF domain to antagonize and thereby decrease the IFN-gamma expression in a MLR as likewise described in Example 6.

Alternatively, in assaying for the ability of an immunomodulatory protein to increase IFN-gamma expression in a primary T-cell assay, a co-immobilization assay can be used as described in Example 6. In a co-immobilization assay, a TCR signal, provided in some embodiments by anti-CD3 antibody, is used in conjunction with a co-immobilized immunomodulatory protein containing an affinity modified IgSF domain to determine the ability to increase IFN-gamma expression relative to an IgSF domain control. In some cases, a soluble form of an immunomodulatory protein that is multimerized to a degree to provide multivalent binding can be employed to determine the ability of the immunomodulatory protein to agonize and thereby increase the IFN-gamma expression in a MLR as likewise described in Example 6.

Use of proper controls is known to those of skill in the art, however, in the aforementioned embodiments, the control typically involves use of the unmodified IgSF domain, such as a wild-type of native IgSF isoform from the same mammalian species from which the IgSF domain was derived or developed. Irrespective of whether the binding affinity to either one or both of cognate binding partners is increased or decreased, a particular immunomodulatory protein in some embodiments will increase IFN-gamma expression and, in alternative embodiments, decrease IFN-gamma expression in a primary T-cell assay relative to a wild-type IgSF domain control.

In some embodiments, an immunomodulatory protein, e.g. containing an affinity modified IgSF domain, increases IFN-gamma expression (i.e., protein expression) relative to a wild-type or unmodified IgSF domain control by at least: 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or higher. In other embodiments, an immunomodulatory protein, e.g. containing an affinity modified IgSF domain, decreases IFN-gamma expression (i.e. protein expression) relative to a wild-type or unmodified IgSF domain control by at least: 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or higher. In some embodiments, an enhancement of immunological activity can be an increase of at least 10%, 20%, 30%, 40%, 50%, 75%, 100%, 200%, 300%, 400%, or 500% greater than a non-zero control value such as in a MLR assay. Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56. In some embodiments, suppression of immunological activity can be a decrease of at least 10%, and up to 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%.

III. Nucleic Acids and Methods of Making Proteins

The present invention provides isolated or recombinant nucleic acids collectively referred to as “nucleic acids of the invention” which encode any of the various embodiments of the immunomodulatory proteins (Type I and Type II) of the invention. Nucleic acids of the invention, including all described below, are useful in recombinant production (e.g., expression) of polypeptides of the invention. The nucleic acids of the invention can be in the form of RNA or in the form of DNA, and include mRNA, cRNA, recombinant or synthetic RNA and DNA, and cDNA. The nucleic acids of the invention are typically DNA molecules, and usually double-stranded DNA molecules. However, single-stranded DNA, single-stranded RNA, double-stranded RNA, and hybrid DNA/RNA nucleic acids or combinations thereof comprising any of the nucleotide sequences of the invention also are provided.

The present invention also relates to expression vectors and host cells useful in producing the immunomodulatory proteins of the present invention. The immunomodulatory proteins of the invention can be made in transformed host cells using recombinant DNA techniques. To do so, a recombinant DNA molecule encoding an immunomodulatory protein is prepared. Methods of preparing such DNA molecules are well known in the art. For instance, sequences coding for the peptides could be excised from DNA using suitable restriction enzymes. Alternatively, the DNA molecule could be synthesized using chemical synthesis techniques, such as the phosphoramidite method. Also, a combination of these techniques could be used. In some instances, a recombinant or synthetic nucleic acid may be generated through polymerase chain reaction (PCR).

The invention also includes expression vectors capable of expressing the immunomodulatory proteins in an appropriate host cell under conditions suited to expression of the immunomodulatory protein. A recombinant expression vector comprises the DNA molecule that codes for the immunomodulatory protein operatively linked to appropriate expression control sequences. Methods of affecting this operative linking, either before or after the DNA molecule is inserted into the vector, are well known. Expression control sequences include promoters, activators, enhancers, operators, ribosomal binding sites, start signals, stop signals, cap signals, polyadenylation signals, and other signals involved with the control of transcription or translation. The resulting recombinant expression vector having the DNA molecule thereon is used to transform an appropriate host. This transformation can be performed using methods well known in the art. In some embodiments, a nucleic acid of the invention further comprises nucleotide sequence that encodes a secretory or signal peptide operably linked to the nucleic acid encoding an immunomodulatory protein of the invention such that the immunomodulatory protein is recovered from the culture medium, host cell, or host cell periplasm.

Any of a large number of available and well-known host cells can be used in the practice of this invention. The selection of a suitable host is dependent upon a number of factors recognized by the art. These include, for example, compatibility with the chosen expression vector, toxicity of the peptides encoded by the DNA molecule, rate of transformation, ease of recovery of the peptides, expression characteristics, bio-safety and costs. A balance of these factors must be struck with the understanding that not all hosts can be equally effective for the expression of a particular DNA sequence. Host cells can be a variety of eukaryotic cells, such as in yeast cells, or with mammalian cells such as Chinese hamster ovary (CHO) or HEK293 cells. Host cells can also be prokaryotic cells, such as with E. coli. The transformed host is cultured under immunomodulatory protein expressing conditions, and then purified. Recombinant host cells can be cultured under conventional fermentation conditions so that the desired immunomodulatory proteins are expressed. Such fermentation conditions are well known in the art. Finally, the immunomodulatory proteins are recovered and purified from recombinant cell cultures by any of a number of methods well known in the art, including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, and affinity chromatography. Protein refolding steps can be used, as desired, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed in the final purification steps. Immunomodulatory proteins of the present invention can also be made by synthetic methods. Solid phase synthesis is the preferred technique of making individual peptides since it is the most cost-effective method of making small peptides. For example, well known solid phase synthesis techniques include the use of protecting groups, linkers, and solid phase supports, as well as specific protection and deprotection reaction conditions, linker cleavage conditions, use of scavengers, and other aspects of solid phase peptide synthesis. Peptides can then be assembled into the immunomodulatory proteins of the present invention.

The means by which the affinity modified IgSF domains of the immunomodulatory invention are designed or created is not limited to any particular method. In some embodiments, however, wild-type IgSF domains are mutagenized (site specific, random, or combinations thereof) from wild-type IgSF genetic material and screened for altered binding according to the methods disclosed in the Examples. Methods or mutagenizing nucleic acids is known to those of skill in the art. In some embodiments, the affinity modified IgSF domains are synthesized de novo utilizing protein or nucleic acid sequences available at any number of publicly available databases and then subsequently screened. The National Center for Biotechnology Information provides such information and its website is publicly accessible via the internet as is the UniProtKB database as discussed previously.

IV. Methods of Screening or Identifying Affinity Modified IgSF Domains

Provided herein is a method of identifying an affinity modified immunomodulatory protein that is capable of binding to two or more cognate binding partners at the same time or in a non-competitive manner. In some embodiments, the method comprises: a) contacting a modified protein comprising at least one non-immunoglobulin modified immunoglobulin superfamily (IgSF) domain or specific binding fragment thereof with at least two cognate binding partners under conditions capable of effecting binding of the protein with the at least two cognate binding partners, wherein the at least one modified IgSF domain comprises one or more amino acid substitutions in a wild-type IgSF domain; b) identifying a modified protein comprising the modified IgSF domain that has increased binding to at least one of the two cognate binding partners compared to a protein comprising the wild-type IgSF domain; and c) selecting a modified protein comprising the modified IgSF domain that binds non-competitively to the at least two cognate binding partners, thereby identifying the affinity modified immunomodulatory protein. In some embodiments, the affinity modified protein that is selected is capable or binding the two cognate binding partners simultaneously at the same time. It is within the level of a skilled artisan to assess or determine the presence of non-competitive binding interactions of a protein for two more different ligands. Exemplary of such methods are described in Example 7.

In some embodiments, the IgSF domain is a non-immunoglobulin IgSF domain. In some embodiments, the modified or variant protein is one in which one or more amino acid substitutions, deletions or insertions have been made in the IgSF domain of any of a non-immunoglobulin IgSF family member, such as any set forth in Table 1. In some embodiments, the modified or variant IgSF domain or the modified protein containing the modified or variant IgSF domain contains at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid changes, such as amino acid substitutions.

In some embodiments, libraries of modified or variant proteins are generated by mutating any one or more amino acid residues of a protein known to contain a non-immunoglobulin IgSF domain using any method commonly known in the art. Any of the methods employed in the art for generating, engineering or diversifying a binding molecule can be used in generating a modified IgSF domain herein. Exemplary of such methods for generating, engineering or diversifying a binding molecule include, but are not limited to, methods described in U.S. Pat. Nos. 5,223,409; 5,571,698, 5,750,373, 5,821,047; 5,837,500; 5,733,743; 5,871,907; 5,969,108; 6,040,136; 6,172,197; 6,291,159; 6,955,877; 6,979,538; 6,831,161; 7,063,943; 7,118,879; 7,208,293; 7,332,571; 7,385,028; 7,696,312; 7,638,299; 7,888,533; 7,642,044; U.S. Patent Application No. US20080300163; US20090208454; US20090155843; US20080113412; US20100035812; US20100093608; US20110015345; For example, an IgSF-contain can be used in methods in place of other binding molecules in methods of diversification or engineering of biomolecules.

Methods for generating libraries of binding molecules and for creating diversity in the library are well known in the art and can be employed to generate libraries of protein variants. Approaches for generating diversity include targeted and non-targeted approaches well known in the art. For example, known approaches for generating diverse nucleic acid and polypeptide libraries include, but are not limited to error-prone PCR, cassette mutagenesis; mutual primer extension; template-assisted ligation and extension; codon cassette mutagenesis; oligonucleotide-directed mutagenesis; amplification using degenerate oligonucleotide primers, including overlap and two-step PCR; and combined approaches, such as combinatorial multiple cassette mutagenesis (CMCM) and related techniques. A skilled artisan is familiar with these techniques.

Examples of methods to mutate a protein to generate libraries of candidate modified protein molecules include methods that result in random mutagenesis across the entire protein sequence or methods that result in mutagenesis of a select region or domain of the protein. Mutations can be introduced randomly, using methods that result in random mutagenesis of the protein, or more systematically, using methods that specifically create single or multiple amino acid change at a targeted position. Both random mutagenesis and systematic site-directed mutagenesis can be used to introduce one or more mutations in the protein. The variant protein can harbor one or more amino acid substitutions, insertions or deletions compared to the wildtype or unmodified protein used as the scaffold to generate the library. The substitutions or insertions can be with any naturally occurring amino acids or non-naturally occurring amino acids.

In methods for identifying or generating a variant or modified protein containing a non-immunoglobulin IgSF domain in accord with the provided methods, one or more regions of the protein, such as an IgSF domain or domains of the protein, can be modified using random mutagenesis of a region to generate one or a plurality of modified protein molecules. For example, a library of variants can be generated containing a plurality of modified molecules that each differ by at least one amino acid replacement (i.e. substitution) deletion or insertion in an IgSF domain compared to a corresponding unmodified or wild-type protein containing the IgSF domain. The amino acid substitution(s) can be substitutions(s) of naturally occurring amino acids or non-naturally occurring amino acids compared to the unmodified or wild-type protein. Generally, the libraries provided herein include libraries containing at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 10², 10³, 10⁴, 2×10⁴, 3×10⁴, 4×10⁴, 5×10⁴, 6×10⁴, 7×10⁴, 8×10⁴, 9×10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹ or more different members. The generated library containing a plurality of modified proteins can be generated as a display library, including a combinatorial library where display of the variant is by, for example, phage display, cell-surface display, bead display, ribosome display, or others. The libraries can be used to screen for modified or variant proteins containing non-immunoglobulin IgSF domains that specifically bind non-competitively to the at least two cognate binding partners.

In some embodiments, prior to selecting a modified protein comprising the modified IgSF domain that binds non-competitively to the at least two cognate binding partners, the method includes combining two or more modified IgSF domain or specific binding fragments thereof identified in step (b) to generate a stacked molecule construct containing a plurality of different modified IgSF domains.

Thus, in some embodiments, provided herein is a method of identifying an affinity modified immunomodulatory protein, comprising: a) contacting a modified protein comprising at least one non-immunoglobulin modified immunoglobulin superfamily (IgSF) domain or specific binding fragment thereof with at least two cognate binding partners under conditions capable of effecting binding of the protein with the at least two cognate binding partners, wherein the at least one modified IgSF domain comprises one or more amino acid substitutions in a wild-type IgSF domain; b) identifying a modified protein comprising the modified IgSF domain that has increased binding to at least one of the two cognate binding partners compared to a protein comprising the wild-type IgSF domain; c) combining two or more modified IgSF domains present in two or more identified proteins to generate a fusion (stacked) protein comprising a first modified IgSF domain linked to a second IgSF domain; and d) selecting a modified protein comprising the modified IgSF domains that binds non-competitively to the at least two cognate binding partners, thereby identifying the affinity modified immunomodulatory protein.

In some embodiments, the at least two cognate binding partners are cell surface molecular species expressed on the surface of a mammalian cell. In some embodiments, the cell surface molecular species are expressed in cis configuration or trans configuration. In some embodiments, the mammalian cell is one of two mammalian cells forming an immunological synapse (IS) and each of the cell surface molecular species is expressed on at least one of the two mammalian cells forming the IS. In some embodiments, at least one of the mammalian cells is a lymphocyte, which can be an NK cell or a T cell. In some embodiments, at least one of the mammalian cells is a tumor cell. In some embodiments, at least one of the mammalian cells is an antigen-presenting cell.

In some embodiments, the two or more cognate binding partners are independently a ligand of an IgSF member selected from CD80, CD86, PD-L1, PD-L2, ICOS Ligand, B7-H3, B7-H4, CD28, CTLA4, PD-1, ICOS, BTLA, CD4, CD8-alpha, CD8-beta, LAG3, TIM-3, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, CD200R or Nkp30. In some embodiments, the two or more cognate binding partners are independently a ligand of a B7 family member. In some embodiments, the two or more cognate binding partners are selected from two or more of CD28, CTLA-4, ICOS or PD-L1.

V. Pharmaceutical Compositions and Formulations

A pharmaceutical composition comprising a therapeutic composition of the invention may contain formulation materials for modifying, maintaining or preserving, for example, the pH, osmolarity, viscosity, clarity, color, isotonicity, odor, sterility, stability, rate of dissolution or release, adsorption, or penetration of the composition. The primary vehicle or carrier in a pharmaceutical composition may be either aqueous or non-aqueous in nature. For example, a suitable vehicle or carrier may be water for injection or physiological saline, possibly supplemented with other materials common in compositions for parenteral administration. Neutral buffered saline or saline mixed with serum albumin are further exemplary vehicles. Other exemplary pharmaceutical compositions comprise Tris buffer of about pH 7.0-8.5, or acetate buffer of about pH 4.0-5.5, which may further include sorbitol or a suitable substitute therefore. In one embodiment of the present invention, binding agent compositions may be prepared for storage by mixing the selected composition having the desired degree of purity with optional formulation agents in the form of a lyophilized cake or an aqueous solution. Further, the binding agent product may be formulated as a lyophilizate using appropriate excipients such as sucrose.

The formulation components are present in concentrations that are acceptable to the site of administration. For example, buffers are used to maintain the composition at physiological pH or at slightly lower pH, typically within a pH range of from about 5 to about 8. A particularly suitable vehicle for parenteral administration is sterile distilled water in which a binding agent is formulated as a sterile, isotonic solution, properly preserved. Yet another preparation can involve the formulation of the desired molecule with an agent, such as injectable microspheres, bio-erodible particles, polymeric compounds (polylactic acid, polyglycolic acid), beads, or liposomes, that provide for the controlled or sustained release of the product which may then be delivered via a depot injection.

In another aspect, pharmaceutical formulations suitable for parenteral administration may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiologically buffered saline. Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Additional pharmaceutical compositions will be evident to those skilled in the art, including formulations involving binding agent molecules in sustained- or controlled-delivery formulations. Techniques for formulating a variety of other sustained- or controlled-delivery means, such as liposome carriers, bio-erodible microparticles or porous beads and depot injections, are also known to those skilled in the art. The pharmaceutical composition to be used for in vivo administration typically must be sterile. This may be accomplished by filtration through sterile filtration membranes. Where the composition is lyophilized, sterilization using this method may be conducted either prior to or following lyophilization and reconstitution. The composition for parenteral administration may be stored in lyophilized form or in solution. In addition, parenteral compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.

In some embodiments, the pharmaceutical composition is sterile. Sterilization may be accomplished by filtration through sterile filtration membranes or radiation. Where the composition is lyophilized, sterilization using this method may be conducted either prior to or following lyophilization and reconstitution. The composition for parenteral administration may be stored in lyophilized form or in solution. In addition, parenteral compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.

Once the pharmaceutical composition has been formulated, it may be stored in sterile vials as a solution, suspension, gel, emulsion, solid, or a dehydrated or lyophilized powder. Such formulations may be stored either in a ready-to-use form or in a form (e.g., lyophilized) requiring reconstitution prior to administration. An effective amount of a pharmaceutical composition to be employed therapeutically will depend, for example, upon the therapeutic context and objectives. One skilled in the art will appreciate that the appropriate dosage levels for treatment will thus vary depending, in part, upon the molecule delivered, the indication for which the binding agent molecule is being used, the route of administration, and the size (body weight, body surface or organ size) and condition (the age and general health) of the patient. Accordingly, the clinician may titer the dosage and modify the route of administration to obtain the optimal therapeutic effect. The therapeutic composition of the invention can be administered parentally, subcutaneously, or intravenously, or as described elsewhere herein. The therapeutic composition of the invention may be administered in a therapeutically effective amount one, two, three or four times per month, two times per week, biweekly (every two weeks), or bimonthly (every two months). Administration may last for a period of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months or longer (e.g., one, two, three, four or more years, including for the life of the subject).

Generally, dosages and routes of administration of the pharmaceutical composition are determined according to the size and condition of the subject, according to standard pharmaceutical practice. For example, the therapeutically effective dose can be estimated initially either in cell culture assays or in animal models such as mice, rats, rabbits, dogs, pigs, or monkeys. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. The exact dosage will be determined in light of factors related to the subject requiring treatment. Dosage and administration are adjusted to provide sufficient levels of the active compound or to maintain the desired effect. Factors that may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy.

In some embodiments, the pharmaceutical composition is administered to a subject through any route, including orally, transdermally, by inhalation, intravenously, intra-arterially, intramuscularly, direct application to a wound site, application to a surgical site, intraperitoneally, by suppository, subcutaneously, intradermally, transcutaneously, by nebulization, intrapleurally, intraventricularly, intra-articularly, intraocularly, or intraspinally.

In some embodiments, the dosage of the pharmaceutical composition is a single dose or a repeated dose. In some embodiments, the doses are given to a subject once per day, twice per day, three times per day, or four or more times per day. In some embodiments, about 1 or more (such as about 2 or more, about 3 or more, about 4 or more, about 5 or more, about 6 or more, or about 7 or more) doses are given in a week. In some embodiments, multiple doses are given over the course of days, weeks, months, or years. In some embodiments, a course of treatment is about 1 or more doses (such as about 2 or more does, about 3 or more doses, about 4 or more doses, about 5 or more doses, about 7 or more doses, about 10 or more doses, about 15 or more doses, about 25 or more doses, about 40 or more doses, about 50 or more doses, or about 100 or more doses).

In some embodiments, an administered dose of the pharmaceutical composition is about 1 μg of protein per kg subject body mass or more (such as about 2 μg of protein per kg subject body mass or more, about 5 μg of protein per kg subject body mass or more, about 10 μg of protein per kg subject body mass or more, about 25 μg of protein per kg subject body mass or more, about 50 μg of protein per kg subject body mass or more, about 100 μg of protein per kg subject body mass or more, about 250 μg of protein per kg subject body mass or more, about 500 μg of protein per kg subject body mass or more, about 1 mg of protein per kg subject body mass or more, about 2 mg of protein per kg subject body mass or more, or about 5 mg of protein per kg subject body mass or more).

For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays or in animal models such as mice, rats, rabbits, dogs, pigs, or monkeys. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. The exact dosage will be determined in light of factors related to the subject requiring treatment. Dosage and administration are adjusted to provide sufficient levels of the active compound or to maintain the desired effect. Factors that may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy. Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation. The frequency of dosing will depend upon the pharmacokinetic parameters of the molecule in the formulation used. Typically, a composition is administered until a dosage is reached that achieves the desired effect. The composition may therefore be administered as a single dose, or as multiple doses (at the same or different concentrations/dosages) over time, or as a continuous infusion. Further refinement of the appropriate dosage is routinely made. Appropriate dosages may be ascertained through use of appropriate dose-response data.

In some embodiments, one or more biomarkers or physiological markers for therapeutic effect can be monitored including T cell activation or proliferation, cytokine synthesis or production (e.g., production of TNF-α, IFN-γ, IL-2), induction of various activation markers (e.g., CD25, IL-2 receptor), inflammation, joint swelling or tenderness, serum level of C-reactive protein, anti-collagen antibody production, and/or T cell-dependent antibody response(s).

An injectable pharmaceutical composition comprising a suitable pharmaceutically acceptable excipient or carrier (e.g., PBS) and an effective amount of a therapeutic composition of the invention can be administered parenterally, intramuscularly, intraperitoneally, intravenously, subdermally, transdermally, subcutaneously, or intradermally to a mammalian patient. Administration can be facilitated via liposomes. The skin and muscle are generally preferred targets for administration of the therapeutic composition of the invention, by any suitable technique. Thus, the delivery of the therapeutic composition of the invention into or through the skin of a mammalian subject (e.g., human), is a feature of the invention. Such molecules of the invention can be administered in a pharmaceutically acceptable injectable solution into or through the skin, e.g., intramuscularly, or intraperitoneally. Administration can also be accomplished by transdermal devices, or, more typically, biolistic delivery of the therapeutic composition of the invention into, or through the skin of the subject or into exposed muscle of the mammalian subject.

A variety of means are known for determining if administration of a therapeutic composition of the invention sufficiently modulates immunological activity by eliminating, sequestering, or inactivating immune cells mediating or capable of mediating an undesired immune response; inducing, generating, or turning on immune cells that mediate or are capable of mediating a protective immune response; changing the physical or functional properties of immune cells; or a combination of these effects. Examples of measurements of the modulation of immunological activity include, but are not limited to, examination of the presence or absence of immune cell populations (using flow cytometry, immunohistochemistry, histology, electron microscopy, polymerase chain reaction (PCR)); measurement of the functional capacity of immune cells including ability or resistance to proliferate or divide in response to a signal (such as using T cell proliferation assays and pepscan analysis based on 3H-thymidine incorporation following stimulation with anti-CD3 antibody, anti-T cell receptor antibody, anti-CD28 antibody, calcium ionophores, PMA, antigen presenting cells loaded with a peptide or protein antigen; B cell proliferation assays); measurement of the ability to kill or lyse other cells (such as cytotoxic T cell assays); measurements of the cytokines, chemokines, cell surface molecules, antibodies and other products of the cells (e.g., by flow cytometry, enzyme-linked immunosorbent assays, Western blot analysis, protein microarray analysis, immunoprecipitation analysis); measurement of biochemical markers of activation of immune cells or signaling pathways within immune cells (e.g., Western blot and immunoprecipitation analysis of tyrosine, serine or threonine phosphorylation, polypeptide cleavage, and formation or dissociation of protein complexes; protein array analysis; DNA transcriptional, profiling using DNA arrays or subtractive hybridization); measurements of cell death by apoptosis, necrosis, or other mechanisms (e.g., annexin V staining, TUNEL assays, gel electrophoresis to measure DNA laddering, histology; fluorogenic caspase assays, Western blot analysis of caspase substrates); measurement of the genes, proteins, and other molecules produced by immune cells (e.g., Northern blot analysis, polymerase chain reaction, DNA microarrays, protein microarrays, 2-dimensional gel electrophoresis, Western blot analysis, enzyme linked immunosorbent assays, flow cytometry); and measurement of clinical symptoms or outcomes such as improvement of autoimmune, neurodegenerative, and other diseases involving self proteins or self polypeptides (clinical scores, requirements for use of additional therapies, functional status, imaging studies) for example, by measuring relapse rate or disease severity (using clinical scores known to the ordinarily skilled artisan) in the case of multiple sclerosis, measuring blood glucose in the case of type I diabetes, or joint inflammation in the case of rheumatoid arthritis.

Also provided herein are articles of manufacture comprising the pharmaceutical compositions described herein in suitable packaging. Suitable packaging for compositions (such as ophthalmic compositions) described herein are known in the art, and include, for example, vials (such as sealed vials), vessels, ampules, bottles, jars, flexible packaging (e.g., sealed Mylar or plastic bags), and the like. These articles of manufacture may further be sterilized and/or sealed.

Further provided are kits comprising the pharmaceutical compositions (or articles of manufacture) described herein, which may further comprise instruction(s) on methods of using the composition, such as uses described herein. The kits described herein may also include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for performing any methods described herein.

VI. Therapeutic Applications

Immunomodulatory proteins of the invention are believed to have utility in a variety of applications, including, but not limited to, e.g., in prophylactic or therapeutic methods (collectively, a “therapeutic composition of the invention”) for treating a variety of immune system diseases or conditions in a mammal in which modulation or regulation of the immune system and immune system responses is beneficial. For example, suppressing an immune response can be beneficial in prophylactic and/or therapeutic methods for inhibiting rejection of a tissue, cell, or organ transplant from a donor by a recipient. In a therapeutic context, the mammalian subject is typically one with an immune system disease or condition, and administration is conducted to prevent further progression of the disease or condition. For example, administration of a therapeutic composition of the invention to a subject suffering from an immune system disease (e.g., autoimmune disease) can result in suppression or inhibition of such immune system attack or biological responses associated therewith. By suppressing this immune system attack on healthy body tissues, the resulting physical symptoms (e.g., pain, joint inflammation, joint swelling or tenderness) resulting from or associated with such attack on healthy tissues can be decreased or alleviated, and the biological and physical damage resulting from or associated with the immune system attack can be decreased, retarded, or stopped. In a prophylactic context, the subject may be one with, susceptible to, or believed to present an immune system disease, disorder or condition, and administration is typically conducted to prevent progression of the disease, disorder or condition, inhibit or alleviate symptoms, signs, or biological responses associated therewith, prevent bodily damage potentially resulting therefrom, and/or maintain or improve the subject's physical functioning.

The immune system disease or disorder of the patient may be or involve, e.g., but is not limited to, Addison's Disease, Allergy, Alopecia Areata, Alzheimer's, Antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis, Ankylosing Spondylitis, Antiphospholipid Syndrome (Hughes Syndrome), arthritis, Asthma, Atherosclerosis, Atherosclerotic plaque, autoimmune disease (e.g., lupus, RA, MS, Graves' disease, etc.), Autoimmune Hemolytic Anemia, Autoimmune Hepatitis, Autoimmune inner ear disease, Autoimmune Lymphoproliferative syndrome, Autoimmune Myocarditis, Autoimmune Oophoritis, Autoimmune Orchitis, Azoospermia, Behcet's Disease, Berger's Disease, Bullous Pemphigoid, Cardiomyopathy, Cardiovascular disease, Celiac Sprue/Coeliac disease, Chronic Fatigue Immune Dysfunction Syndrome (CFIDS), Chronic idiopathic polyneuritis, Chronic Inflammatory Demyelinating, Polyradicalneuropathy (CIPD), Chronic relapsing polyneuropathy (Guillain-Barré syndrome), Churg-Strauss Syndrome (CSS), Cicatricial Pemphigoid, Cold Agglutinin Disease (CAD), COPD, CREST syndrome, Crohn's disease, Dermatitis, Herpetiformus, Dermatomyositis, diabetes, Discoid Lupus, Eczema, Epidermolysis bullosa acquisita, Essential Mixed Cryoglobulinemia, Evan's Syndrome, Exopthalmos, Fibromyalgia, Goodpasture's Syndrome, graft-related disease or disorder, Graves' Disease, GVHD, Hashimoto's Thyroiditis, Idiopathic Pulmonary Fibrosis, Idiopathic Thrombocytopenia Purpura (ITP), IgA Nephropathy, immunoproliferative disease or disorder (e.g., psoriasis), Inflammatory bowel disease (IBD), Insulin Dependent Diabetes Mellitus (IDDM), Interstitial lung disease, juvenile diabetes, Juvenile Arthritis, juvenile idiopathic arthritis (JIA), Kawasaki's Disease, Lambert-Eaton Myasthenic Syndrome, Lichen Planus, lupus, Lupus Nephritis, Lymphoscytic Lypophisitis, Ménière's Disease, Miller Fish Syndrome/acute disseminated encephalomyeloradiculopathy, Mixed Connective Tissue Disease, Multiple Sclerosis (MS), muscular rheumatism, Myalgic encephalomyelitis (ME), Myasthenia Gravis, Ocular Inflammation, Pemphigus Foliaceus, Pemphigus Vulgaris, Pernicious Anaemia, Polyarteritis Nodosa, Polychondritis, Polyglandular Syndromes (Whitaker's syndrome), Polymyalgia Rheumatica, Polymyositis, Primary Agammaglobulinemia, Primary Biliary Cirrhosis/Autoimmune cholangiopathy, Psoriasis, Psoriatic arthritis, Raynaud's Phenomenon, Reiter's Syndrome/Reactive arthritis, Restenosis, Rheumatic Fever, rheumatic disease, Rheumatoid Arthritis, Sarcoidosis, Schmidt's syndrome, Scleroderma, Sjörgen's Syndrome, Solid-organ transplant rejection (kidney, heart, liver, lung, etc.), Stiff-Man Syndrome, Systemic Lupus Erythematosus (SLE), systemic scleroderma, Takayasu Arteritis, Temporal Arteritis/Giant Cell Arteritis, Thyroiditis, Type 1 diabetes, Type 2 diabetes, Ulcerative colitis, Uveitis, Vasculitis, Vitiligo, Wegener's Granulomatosis, and preventing or suppressing an immune response associated with rejection of a donor tissue, cell, graft, or organ transplant by a recipient subject. Graft-related diseases or disorders include graft versus host disease (GVDH), such as associated with bone marrow transplantation, and immune disorders resulting from or associated with rejection of organ, tissue, or cell graft transplantation (e.g., tissue or cell allografts or xenografts), including, e.g., grafts of skin, muscle, neurons, islets, organs, parenchymal cells of the liver, etc. With regard to a donor tissue, cell, graft or solid organ transplant in a recipient subject, it is believed that a therapeutic composition of the invention disclosed herein may be effective in preventing acute rejection of such transplant in the recipient and/or for long-term maintenance therapy to prevent rejection of such transplant in the recipient (e.g., inhibiting rejection of insulin-producing islet cell transplant from a donor in the subject recipient suffering from diabetes).

A therapeutic composition of the invention can also be used to inhibit growth of mammalian, particularly human, cancer cells as a monotherapy (i.e., as a single agent), in combination with at least one chemotherapeutic agent (i.e., a combination therapy), in combination with a cancer vaccine, in combination with an immune checkpoint inhibitor and/or in combination with radiation therapy. In some aspects of the present disclosure, the immune checkpoint inhibitor is nivolumab, tremelimumab, pembrolizumab, ipilimumab, or the like. An effective amount of a therapeutic composition is administered to inhibit, halt, or reverse progression of cancers that are sensitive to modulation of immunological activity by immunomodulatory proteins of the present invention. Human cancer cells can be treated in vivo, or ex vivo. In ex vivo treatment of a human patient, tissue or fluids containing cancer cells are treated outside the body and then the tissue or fluids are reintroduced back into the patient. In some embodiments, the cancer is treated in a human patient in vivo by administration of the therapeutic composition into the patient. Thus, the present invention provides ex vivo and in vivo methods to inhibit, halt, or reverse progression of the tumor, or otherwise result in a statistically significant increase in progression-free survival (i.e., the length of time during and after treatment in which a patient is living with cancer that does not get worse), or overall survival (also called “survival rate;” i.e., the percentage of people in a study or treatment group who are alive for a certain period of time after they were diagnosed with or treated for cancer) relative to treatment with a control. The cancers which can be treated by the methods of the invention include, but are not limited to, melanoma, bladder cancer, hematological malignancies (leukemia, lymphoma, myeloma), liver cancer, brain cancer, renal cancer, breast cancer, pancreatic cancer (adenocarcinoma), colorectal cancer, lung cancer (small cell lung cancer and non-small-cell lung cancer), spleen cancer, cancer of the thymus or blood cells (i.e., leukemia), prostate cancer, testicular cancer, ovarian cancer, uterine cancer, gastric carcinoma, or Ewing's sarcoma.

VII. Exemplary Embodiments

Among the provided embodiments are:

Embodiment 1

In some embodiments, there is provided an immunomodulatory protein, comprising at least one non-immunoglobulin affinity modified immunoglobulin superfamily (IgSF) domain comprising one or more amino acid substitution(s) in a wild-type IgSF domain, wherein: the at least one affinity modified IgSF domain has increased binding to at least two cognate binding partners compared to the wild-type IgSF domain; and the at least one affinity modified IgSF domain specifically binds non-competitively to the at least two cognate binding partners.

Embodiment 2

In some further embodiments of embodiment 1, the at least two cognate binding partners are cell surface molecular species expressed on the surface of a mammalian cell.

Embodiment 3

In some further embodiments of embodiment 2, the cell surface molecular species are expressed in cis configuration or trans configuration.

Embodiment 4

In some further embodiments of embodiment 2 or embodiment 3, the mammalian cell is one of two mammalian cells forming an immunological synapse (IS) and each of the cell surface molecular species is expressed on at least one of the two mammalian cells forming the IS.

Embodiment 5

In some further embodiments of any one of embodiments 2-4, at least one of the mammalian cells is a lymphocyte.

Embodiment 6

In some further embodiments of embodiment 5, the lymphocyte is an NK cell or a T cell.

Embodiment 7

In some further embodiments of any one of embodiments 5-6, binding of the affinity modified IgSF domain modulates immunological activity of the lymphocyte.

Embodiment 8

In some further embodiments of embodiment 7, the immunomodulatory protein is capable of effecting increased immunological activity compared the wild-type protein comprising the wild-type IgSF domain.

Embodiment 9

In some further embodiments of embodiment 7, the immunomodulatory protein is capable of effecting decreased immunological activity compared to the wild-type protein comprising the wild-type IgSF domain.

Embodiment 10

In some further embodiments of any one of embodiments 2-9, at least one of the mammalian cells is a tumor cell.

Embodiment 11

In some further embodiments of any one of embodiments 2-10, the mammalian cells are human cells.

Embodiment 12

In some further embodiments of any one of embodiments 4-11, the affinity modified IgSF domain is capable of specifically binding to the two mammalian cells forming the IS.

Embodiment 13

In some further embodiments of any one of embodiments 1-12, the wild-type IgSF domain is from an IgSF family member of a family selected from Signal-Regulatory Protein (SIRP) Family, Triggering Receptor Expressed On Myeloid Cells Like (TREML) Family, Carcinoembryonic Antigen-related Cell Adhesion Molecule (CEACAM) Family, Sialic Acid Binding Ig-Like Lectin (SIGLEC) Family, Butyrophilin Family, B7 family, CD28 family, V-set and Immunoglobulin Domain Containing (VSIG) family, V-set transmembrane Domain (VSTM) family, Major Histocompatibility Complex (MHC) family, Signaling lymphocytic activation molecule (SLAM) family, Leukocyte immunoglobulin-like receptor (LIR), Nectin (Nec) family, Nectin-like (NECL) family, Poliovirus receptor related (PVR) family, Natural cytotoxicity triggering receptor (NCR) family, T cell immunoglobulin and mucin (TIM) family or Killer-cell immunoglobulin-like receptors (KIR) family.

Embodiment 14

In some further embodiments of any one of embodiments 1-13, the wild-type IgSF domain is from an IgSF member selected from CD80, CD86, PD-L1, PD-L2, ICOS Ligand, B7-H3, B7-H4, CD28, CTLA4, PD-1, ICOS, BTLA, CD4, CD8-alpha, CD8-beta, LAG3, TIM-3, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, CD200R or Nkp30.

Embodiment 15

In some further embodiments of any one of embodiments 1-14, the wild-type IgSF domain is a human IgSF member.

Embodiment 16

In some further embodiments of any one of embodiments 1-15, the wild-type IgSF domain is an IgV domain, an IgC1 domain, an IgC2 domain or a specific binding fragment thereof.

Embodiment 17

In some further embodiments of any one of embodiments 1-16, the affinity-modified IgSF domain is an affinity modified IgV domain, affinity modified IgC1 domain or an affinity modified IgC2 domain or is a specific binding fragment thereof comprising the one or more amino acid substitutions.

Embodiment 18

In some further embodiments of any one of embodiments 1-17, the immunomodulatory protein comprises at least two non-immunoglobulin affinity modified IgSF domains.

Embodiment 19

In some further embodiments of embodiment 18, the at least two non-immunoglobulin affinity modified IgSF domains each comprise one or more different amino acid substitutions in the same wild-type IgSF domain.

Embodiment 20

In some further embodiments of embodiment 19, the at least two non-immunoglobulin affinity modified IgSF domains each comprise one or more amino acid substitutions in different wild-type IgSF domains.

Embodiment 21

In some further embodiments of embodiment 20, the different wild-type IgSF domains are from different IgSF family members.

Embodiment 22

In some further embodiments of any one of embodiments 1-17, the immunomodulatory protein comprises only one non-immunoglobulin affinity modified IgSF domain.

Embodiment 23

In some further embodiments of any one of embodiments 1-22, the affinity-modified IgSF comprises at least 85% sequence identity to a wild-type IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27.

Embodiment 24

In some further embodiments of embodiment 23, the immunomodulatory protein further comprises a second affinity-modified IgSF, wherein the second affinity-modified IgSF domain comprises at least 85% sequence identity to a wild-type IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27.

Embodiment 25

In some further embodiments of any one of embodiments 1-24, the wild-type IgSF domain is a member of the B7 family.

Embodiment 26

In some further embodiments of any one of embodiments 1-25, the wild-type IgSF domain is a domain of CD80, CD86 or ICOSLG.

Embodiment 27

In some further embodiments of any one of embodiments 1-26, the wild-type IgSF domain is a domain of CD80.

Embodiment 28

In some embodiments, there is provided an immunomodulatory protein, comprising at least one affinity modified CD80 immunoglobulin superfamily (IgSF) domain comprising one or more amino acid substitution(s) in a wild-type CD80 IgSF domain, wherein the at least one affinity modified CD80 IgSF domain has increased binding to at least two cognate binding partners compared to the wild-type CD80 IgSF domain.

Embodiment 29

In some further embodiments of embodiment 27 or embodiment 28, the cognate binding partners are CD28 and PD-L1.

Embodiment 30

In some further embodiments of any one of embodiments 27-29, the wild-type IgSF domain is an IgV domain and/or the affinity modified CD80 domain is an affinity modified IgV domain.

Embodiment 31

In some further embodiments of any one of embodiments 27-30, the affinity-modified domain comprises at least 85% sequence identity to a wild-type CD80 domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in SEQ ID NO:1.

Embodiment 32

In some further embodiments of any one of embodiments 1-31, the at least one affinity modified IgSF domain comprises at least 1 and no more than twenty amino acid substitutions in the wild-type IgSF domain.

Embodiment 33

In some further embodiments of any one of embodiments 1-32, the at least one affinity modified IgSF domain comprises at least 1 and no more than ten amino acid substitutions in the wild-type IgSF domain.

Embodiment 34

In some further embodiments of any one of embodiments 1-33, the at least one affinity modified IgSF domain comprises at least 1 and no more than five amino acid substitutions in the wild-type IgSF domain.

Embodiment 35

In some further embodiments of any one of embodiments 1-34, the affinity modified IgSF domain has at least 120% of the binding affinity as its wild-type IgSF domain to each of the at least two cognate binding partners.

Embodiment 36

In some further embodiments of any one of embodiments 1-35, the immunomodulatory protein further comprises a non-affinity modified IgSF domain.

Embodiment 37

In some further embodiments of any one of embodiments 1-36, the immunomodulatory protein is soluble.

Embodiment 38

In some further embodiments of any one of embodiments 1-37, the immunomodulatory protein lacks a transmembrane domain or a cytoplasmic domain.

Embodiment 39

In some further embodiments of any one of embodiments 1-38, the immunomodulatory protein comprises only the extracellular domain (ECD) or a specific binding fragment thereof comprising the affinity modified IgSF domain.

Embodiment 40

In some further embodiments of any one of embodiments 1-39, the immunomodulatory protein is glycosylated or pegylated.

Embodiment 41

In some further embodiments of any one of embodiments 1-40, the immunomodulatory protein is linked to a multimerization domain.

Embodiment 42

In some further embodiments of any one of embodiments 1-41, the immunomodulatory protein is linked to an Fc domain or a variant thereof with reduced effector function.

Embodiment 43

In some further embodiments of embodiment 42, the Fc domain is an IgG1 domain, an IgG2 domain or is a variant thereof with reduced effector function.

Embodiment 44

In some further embodiments of any one of embodiments 39-41, the Fc domain is mammalian, optionally human; or the variant Fc domain comprises one or more amino acid modifications compared to an unmodified Fc domain that is mammalian, optionally human.

Embodiment 45

In some further embodiments of any one of embodiments 42-44, the Fc domain or variant thereof comprises the sequence of amino acids set forth in SEQ ID NO:226 or SEQ ID NO:227 or a sequence of amino acids that exhibits at least 85% sequence identity to SEQ ID NO:226 or SEQ ID NO:227.

Embodiment 46

In some further embodiments of any one of embodiments 38-41, the immunomodulatory protein is linked indirectly via a linker.

Embodiment 47

In some further embodiments of any one of embodiments 41-46, the immunomodulatory protein is a dimer.

Embodiment 48

In some further embodiments of any one of embodiments 1-47, the immunomodulatory protein is attached to a liposomal membrane.

Embodiment 49

In some embodiments, there is provided an immunomodulatory protein, comprising at least two non-immunoglobulin immunoglobulin superfamily (IgSF) domains, wherein: at least one of the non-immunoglobulin modified IgSF domain is affinity-modified to exhibit altered binding to its cognate binding partner; and the at least two non-immunoglobulin modified IgSF domain each independently specifically bind to at least one different cognate binding partner.

Embodiment 50

In some further embodiments of embodiment 49, the each of the at least two non-immunoglobulin IgSF domains are affinity-modified IgSF domains, wherein the first non-immunoglobulin modified IgSF domain comprises one or more amino acid substitutions in a first wild-type-type IgSF domain and the second non-immunoglobulin modified IgSF domain comprises one or more amino acid substitutions in a second wild-type IgSF domain.

Embodiment 51

In some further embodiments of embodiment 50, the first non-immunoglobulin modified IgSF domain exhibits altered binding to at least one of its cognate binding partner(s) compared to the first wild-type IgSF domain; and the second non-immunoglobulin modified IgSF domain exhibits altered binding to at least one of its cognate binding partner(s) compared to the second wild-type IgSF domain.

Embodiment 52

In some further embodiments of any one of embodiments 49-51, the different cognate binding partners are cell surface molecular species expressed on the surface of a mammalian cell.

Embodiment 53

In some further embodiments of embodiment 52, the different cell surface molecular species are expressed in cis configuration or trans configuration.

Embodiment 54

In some further embodiments of embodiment 52 or embodiment 53, the mammalian cell is one of two mammalian cells forming an immunological synapse (IS) and the different cell surface molecular species is expressed on at least one of the two mammalian cells forming the IS.

Embodiment 55

In some further embodiments of any one of embodiments 52-54, at least one of the mammalian cells is a lymphocyte.

Embodiment 56

In some further embodiments of embodiment 55, the lymphocyte is an NK cell or a T cell.

Embodiment 57

In some further embodiments of embodiment 55 or embodiment 56, binding of the immunomodulatory protein to the cell modulates the immunological activity of the lymphocyte.

Embodiment 58

In some further embodiments of embodiment 57, the immunomodulatory protein is capable of effecting increased immunological activity compared to the wild-type protein comprising the wild-type IgSF domain.

Embodiment 59

In some further embodiments of embodiment 57, the immunomodulatory protein is capable of effecting decreased immunological activity compared to the wild-type protein comprising the wild-type IgSF domain.

Embodiment 60

In some further embodiments of any one of embodiments 52-59, at least one of the mammalian cells is a tumor cell.

Embodiment 61

In some further embodiments of any one of embodiments 52-60, the mammalian cells are human cells.

Embodiment 62

In some further embodiments of any one of embodiments 54-61, the immunomodulatory protein is capable of specifically binding to the two mammalian cells forming the IS.

Embodiment 63

In some further embodiments of any one of embodiments 49-62, the first and second modified IgSF domains each comprise one or more amino acid substitutions in different wild-type IgSF domains.

Embodiment 64

In some further embodiments of embodiment 63, the different wild-type IgSF domains are from different IgSF family members.

Embodiment 65

In some further embodiments of any one of embodiments 49-64, the first and second modified IgSF domains are non-wild-type combinations.

Embodiment 66

In some further embodiments of any one of embodiments 49-65, the first wild-type IgSF domain and second wild-type IgSF domain each individually is from an IgSF family member of a family selected from Signal-Regulatory Protein (SIRP) Family, Triggering Receptor Expressed On Myeloid Cells Like (TREML) Family, Carcinoembryonic Antigen-related Cell Adhesion Molecule (CEACAM) Family, Sialic Acid Binding Ig-Like Lectin (SIGLEC) Family, Butyrophilin Family, B7 family, CD28 family, V-set and Immunoglobulin Domain Containing (VSIG) family, V-set transmembrane Domain (VSTM) family, Major Histocompatibility Complex (MHC) family, Signaling lymphocytic activation molecule (SLAM) family, Leukocyte immunoglobulin-like receptor (LIR), Nectin (Nec) family, Nectin-like (NECL) family, Poliovirus receptor related (PVR) family, Natural cytotoxicity triggering receptor (NCR) family, T cell immunoglobulin and mucin (TIM) family or Killer-cell immunoglobulin-like receptors (KIR) family.

Embodiment 67

In some further embodiments of any one of embodiments 49-66, the first wild-type IgSF domain and second wild-type IgSF domain each individually is from an IgSF member selected from CD80, CD86, PD-L1, PD-L2, ICOS Ligand, B7-H3, B7-H4, CD28, CTLA4, PD-1, ICOS, BTLA, CD4, CD8-alpha, CD8-beta, LAG3, TIM-3, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, CD200R or Nkp30.

Embodiment 68

In some further embodiments of any one of embodiments 49-67, the first modified IgSF domain and the second modified IgSF domain each individually comprises at least 85% sequence identity to a wild-type IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27.

Embodiment 69

In some further embodiments of any one of embodiments 49-68, the first and second wild-type IgSF domain each individually is a member of the B7 family.

Embodiment 70

In some further embodiments of embodiment 69, the first and second wild-type IgSF domain each individually is from CD80, CD86 or ICOSLG.

Embodiment 71

In some further embodiments of any one of embodiments 49-68, the first or second wild-type IgSF domain is from a member of the B7 family and the other of the first or second wild-type IgSF domain is from another IgSF family.

Embodiment 72

In some further embodiments of any one of embodiments 49-68 and 71, the first and second wild-type IgSF domain is from ICOSLG and NKp30.

Embodiment 73

In some further embodiments of any one of embodiments 49-68 and 71, the first and second wild-type IgSF domain is from CD80 and NKp30.

Embodiment 74

In some further embodiments of any one of embodiments 49-73, the first and second wild-type IgSF domain each individually is a human IgSF member.

Embodiment 75

In some further embodiments of any one of embodiments 49-74, the first and second wild-type IgSF domain each individually is an IgV domain, and IgC1 domain, an IgC2 domain or a specific binding thereof.

Embodiment 76

In some further embodiments of any one of embodiments 49-75, the first non-immunoglobulin modified domain and the second non-immunoglobulin modified domain each individually is a modified IgV domain, modified IgC1 domain or a modified IgC2 domain or is a specific binding fragment thereof comprising the one or more amino acid substitutions.

Embodiment 77

In some further embodiments of any one of embodiments 49-76, at least one of the first non-immunoglobulin modified domain or the second non-immunoglobulin modified domain is a modified IgV domain.

Embodiment 78

In some further embodiments of any one of embodiments 49-77, the first non-immunoglobulin modified IgSF domain and the second non-immunoglobulin modified IgSF domain each individually comprise 1 and no more than twenty amino acid substitutions.

Embodiment 79

In some further embodiments of any one of embodiments 49-78, the first non-immunoglobulin modified IgSF domain and the second non-immunoglobulin modified IgSF domain each individually comprise 1 and no more than ten amino acid substitutions.

Embodiment 80

In some further embodiments of any one of embodiments 49-79, the first non-immunoglobulin modified IgSF domain and the second non-immunoglobulin modified IgSF domain each individually comprise 1 and no more than five amino acid substitutions.

Embodiment 81

In some further embodiments of any one of embodiments 49-80, at least one of the first or second non-immunoglobulin modified IgSF domain has between 10% and 90% of the binding affinity of the wild-type IgSF domain to at least one of its cognate binding partner.

Embodiment 82

In some further embodiments of any one of embodiments 49-81, at least one of the first of second non-immunoglobulin modified IgSF domain has at least 120% of the binding affinity of the wild-type IgSF domain to at least one of its cognate binding partner.

Embodiment 83

In some further embodiments of any one of embodiments 49-80 and 82, the first and second non-immunoglobulin modified IgSF domain each individually has at least 120% of the binding affinity of the wild-type IgSF domain to at least one of its cognate binding partner.

Embodiment 84

In some further embodiments of any one of embodiments 49-83, the immunomodulatory protein is soluble.

Embodiment 85

In some further embodiments of any one of embodiments 49-84, the immunomodulatory protein is glycosylated or pegylated.

Embodiment 86

In some further embodiments of any one of embodiments 49-85, the immunomodulatory protein is linked to a multimerization domain.

Embodiment 87

In some further embodiments of any one of embodiments 49-86, the immunomodulatory protein is linked to an Fc domain or a variant thereof with reduced effector function.

Embodiment 88

In some further embodiments of embodiment 87, the Fc domain is an IgG1 domain, an IgG2 domain or is a variant thereof with reduced effector function.

Embodiment 89

In some further embodiments of embodiment 87 or embodiment 88, the Fc domain is mammalian, optionally human; or the variant Fc domain comprises one or more amino acid modifications compared to an unmodified Fc domain that is mammalian, optionally human.

Embodiment 90

In some further embodiments of any one of embodiments 87-89, the Fc domain or variant thereof comprises the sequence of amino acids set forth in SEQ ID NO:226 or SEQ ID NO:227 or a sequence of amino acids that exhibits at least 85% sequence identity to SEQ ID NO:226 or SEQ ID NO:227.

Embodiment 91

In some further embodiments of any one of embodiments 86-90, the variant CD80 polypeptide is linked indirectly via a linker.

Embodiment 92

In some further embodiments of any one of embodiments 86-91, the immunomodulatory protein is a dimer.

Embodiment 93

In some further embodiments of any one of embodiments 49-92, the immunomodulatory protein further comprises one or more additional non-immunoglobulin IgSF domain that is the same of different from the first or second non-immunoglobulin modified IgSF domain.

Embodiment 94

In some further embodiments of embodiment 93, the one or more additional non-immunoglobulin IgSF domain is an affinity modified IgSF domain.

Embodiment 95

In some further embodiments of any one of embodiment 49-94, the immunomodulatory protein is attached to a liposomal membrane.

Embodiment 96

In some embodiments, there is provided a nucleic acid molecule, encoding the immunomodulatory polypeptide of any of embodiments 1-95.

Embodiment 97

In some further embodiments of embodiment 96, the nucleic acid is synthetic nucleic acid.

Embodiment 98

In some further embodiments of embodiment 96 or embodiment 97, the nucleic acid is cDNA.

Embodiment 99

In some embodiments, there is provided a vector, comprising the nucleic acid molecule of any of embodiments 96-98.

Embodiment 100

In some further embodiments of embodiment 99, the vector is an expression vector.

Embodiment 101

In some embodiments, there is provided a cell, comprising the vector of embodiment 99 or embodiment 100.

Embodiment 102

In some further embodiments of embodiment 101, the cell is a eukaryotic cell or prokaryotic cell.

Embodiment 103

In some embodiments, there is provided a method of producing an immunomodulatory protein, comprising introducing the nucleic acid molecule of any of embodiments 96-98 or vector of embodiment 99 or embodiment 100 into a host cell under conditions to express the protein in the cell.

Embodiment 104

In some further embodiments of embodiment 103, the method further comprises isolating or purifying the immunomodulatory protein from the cell.

Embodiment 105

In some embodiments, there is provided a pharmaceutical composition, comprising the immunomodulatory protein of any of embodiments 1-95.

Embodiment 106

In some further embodiments of embodiment 105, the pharmaceutical composition comprises a pharmaceutically acceptable excipient.

Embodiment 107

In some further embodiments of embodiment 105 or embodiment 106, the pharmaceutical composition is sterile.

Embodiment 108

In some embodiments, there is provided an article of manufacture comprising the pharmaceutical composition of any of embodiments 105-107 in a vial.

Embodiment 109

In some further embodiments of embodiment 108, the vial is sealed.

Embodiment 110

In some embodiments, there is provided a kit comprising the pharmaceutical composition of any of embodiments 105-107, and instructions for use.

Embodiment 111

In some embodiments, there is provided a kit comprising the article of manufacture according to embodiment 108 or embodiment 109, and instructions for use.

Embodiment 112

In some embodiments, there is provided a method of modulating an immune response in a subject, comprising administering therapeutically effective amount of the immunomodulatory protein of any of embodiments 1-95 to the subject.

Embodiment 113

In some further embodiments of embodiment 112, modulating the immune response treats a disease or condition in the subject.

Embodiment 114

In some further embodiments of embodiment 112 or embodiment 113, the immune response is increased.

Embodiment 115

In some further embodiments of embodiment 114, the disease or condition is a tumor or cancer.

Embodiment 116

In some further embodiments of embodiment 114 or embodiment 115, the disease or condition is selected from melanoma, lung cancer, bladder cancer or a hematological malignancy.

Embodiment 117

In some further embodiments of embodiment 112 or embodiment 113, the immune response is decreased.

Embodiment 118

In some further embodiments of embodiment 117, the disease or condition is an inflammatory disease or condition.

Embodiment 119

In some further embodiments of embodiment 117 or embodiment 118, the disease or condition is selected from Crohn's disease, ulcerative colitis, multiple sclerosis, asthma, rheumatoid arthritis, or psoriasis.

Embodiment 120

In some embodiments, there is provided a method of identifying an affinity modified immunomodulatory protein, comprising: a) contacting a modified protein comprising at least one non-immunoglobulin modified immunoglobulin superfamily (IgSF) domain or specific binding fragment thereof with at least two cognate binding partners under conditions capable of effecting binding of the protein with the at least two cognate binding partners, wherein the at least one modified IgSF domain comprises one or more amino acid substitutions in a wild-type IgSF domain; b) identifying a modified protein comprising the modified IgSF domain that has increased binding to at least one of the two cognate binding partners compared to a protein comprising the wild-type IgSF domain; and c) selecting a modified protein comprising the modified IgSF domain that binds non-competitively to the at least two cognate binding partners, thereby identifying the affinity modified immunomodulatory protein.

Embodiment 121

In some further embodiments of embodiment 120, step b) comprises identifying a modified protein comprising a modified IgSF domain that has increased binding to each of the at least two cognate binding partners compared to a protein comprising the wild-type domain.

Embodiment 122

In some further embodiments of embodiment 120 or embodiment 121, prior to step a), introducing one or more amino acid substitutions into the wild-type IgSF domain, thereby generating a modified protein comprising the modified IgSF domain.

Embodiment 123

In some further embodiments of any one of embodiments 120-122, the modified protein comprises at least two modified IgSF domains or specific binding fragments thereof, wherein the first IgSF domain comprises one or more amino acid substitutions in a first wild-type-type IgSF domain and the second non-immunoglobulin affinity modified IgSF domain comprises one or more amino acid substitutions in a second wild-type IgSF domain.

Embodiment 124

In some further embodiments of embodiment 123, the first and second non-immunoglobulin affinity modified IgSF domain each specifically bind to at least one different cognate binding partner.

Embodiment 125

In some embodiments, there is provided an immunomodulatory protein comprising at least one non-immunoglobulin affinity-modified immunoglobulin superfamily (IgSF) domain, wherein the affinity-modified IgSF domain specifically binds non-competitively to at least two cell-surface molecular species, wherein each of the molecular species is expressed on at least one of the two mammalian cells forming an immunological synapse (IS), wherein one of the mammalian cells is a lymphocyte and wherein binding of the affinity-modified IgSF domain modulates immunological activity of the lymphocyte.

Embodiment 126

In some further embodiments of embodiment 125, the affinity modified IgSF domain specifically binds to the two mammalian cells forming the IS.

Embodiment 127

In some further embodiments of embodiment 125 or embodiment 126, the immunomodulatory protein comprises at least two non-immunoglobulin affinity modified IgSF domains and the immunomodulatory protein specifically binds to the two mammalian cells forming the IS.

Embodiment 128

In some further embodiments of any one of embodiments 125-127, the IgSF cell surface molecular species are human IgSF members.

Embodiment 129

In some further embodiments of any one of embodiments 125-128, the affinity modified IgSF domain comprises at least one affinity modified human CD80 domain.

Embodiment 130

In some further embodiments of any one of embodiments 125-129, the immunomodulatory protein comprises an affinity modified mammalian IgSF member.

Embodiment 131

In some further embodiments of any one of embodiments 125-130, the affinity modified mammalian IgSF member is at least one of: CD80, PVR, ICOSLG, or HAVCR2.

Embodiment 132

In some further embodiments of any one of embodiments 125-131, immunological activity is enhanced.

Embodiment 133

In some further embodiments of any one of embodiments 125-132, immunological activity is suppressed.

Embodiment 134

In some further embodiments of any one of embodiments 125-133, one of the two mammalian cells is a tumor cell.

Embodiment 135

In some further embodiments of any one of embodiments 125-134, the lymphocyte is an NK cell or a T-cell.

Embodiment 136

In some further embodiments of any one of embodiments 125-135, the mammalian cells are a mouse, rat, cynomologus monkey, or human cells.

Embodiment 137

In some further embodiments of any one of embodiments 125-136, the affinity modified IgSF domain has between 10% and 90% of the binding affinity of the wild-type IgSF domain to at least one of the two cell surface molecular species.

Embodiment 138

In some further embodiments of any one of embodiments 125-137, the affinity modified IgSF domain specifically binds non-competitively to exactly one IgSF member.

Embodiment 139

In some further embodiments of any one of embodiments 125-138, the affinity modified IgSF domain has at least 120% of the binding affinity as its wild-type IgSF domain to at least one of the two cell surface molecular species.

Embodiment 140

In some further embodiments of any one of embodiments 125-139, the affinity modified IgSF domain is an affinity modified IgV, IgC1, or IgC2 domain.

Embodiment 141

In some further embodiments of any one of embodiments 125-140, the affinity modified IgSF domain differs by at least one and no more than ten amino acid substitutions from its wild-type IgSF domain.

Embodiment 142

In some further embodiments of any one of embodiments 125-141, the affinity modified IgSF domain differs by at least one and no more than five amino acid substitutions from its wild-type IgSF domain.

Embodiment 143

In some further embodiments of any one of embodiments 125-142, the affinity modified IgSF domain is a human CD80 IgSF domain.

Embodiment 144

In some further embodiments of any one of embodiments 125-143, the immunomodulatory protein comprises at least two affinity-modified IgSF domains, wherein the affinity modified IgSF domains are not the same species of IgSF domain.

Embodiment 145

In some further embodiments of any one of embodiments 125-144, the immunomodulatory protein is covalently bonded, directly or indirectly, to an antibody fragment crystallizable (Fc).

Embodiment 146

In some further embodiments of any one of embodiments 125-145, the immunomodulator protein is in a pharmaceutically acceptable carrier.

Embodiment 147

In some further embodiments of any one of embodiments 125-146, the immunomodulatory protein is glycosylated or pegylated.

Embodiment 148

In some further embodiments of any one of embodiments 125-147, the immunomodulatory protein is soluble.

Embodiment 149

In some further embodiments of any one of embodiments 125-148, the immunomodulatory protein is attached to a liposomal membrane.

Embodiment 150

In some further embodiments of any one of embodiments 125-149, the immunomodulatory protein is dimerized by intermolecular disulfide bonds.

Embodiment 151

In some further embodiments of any one of embodiments 125-150, the cell surface molecular species are expressed in cis configuration or trans configuration.

Embodiment 152

In some embodiments, there is provided an immunomodulatory protein comprising at least two non-immunoglobulin affinity-modified immunoglobulin superfamily (IgSF) domains, wherein the affinity-modified IgSF domains each specifically binds to a different cell surface molecular species, wherein each of the molecular species is expressed on at least one of the two mammalian cells forming an immunological synapse (IS), wherein one of the mammalian cells is a lymphocyte, and wherein binding of the affinity-modified IgSF domain modulates immunological activity of the lymphocyte.

Embodiment 153

In some further embodiments of any one of embodiments 125-152, at least one of the affinity modified IgSF domains binds competitively.

Embodiment 154

In some further embodiments of any one of embodiments 125-153, the affinity modified IgSF domains are not the same species of IgSF domain.

Embodiment 155

In some further embodiments of any one of embodiments 125-154, the affinity modified IgSF domains are non-wild type combinations.

Embodiment 156

In some further embodiments of any one of embodiments 125-155, the cell surface molecular species are human IgSF members.

Embodiment 157

In some further embodiments of any one of embodiments 125-156, the at least two affinity modified IgSF domains are from at least one of: CD80, CD86, CD274, PDCD1LG2, ICOSLG, CD276, VTCN1, CD28, CTLA4, PDCD1, ICOS, BTLA, CD4, CD8A, CD8B, LAG3, HAVCR2, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, or CD200R1.

Embodiment 158

In some further embodiments of any one of embodiments 125-157, the immunomodulatory protein comprises at least two affinity modified mammalian IgSF members.

Embodiment 159

In some further embodiments of any one of embodiments 125-158, the mammalian IgSF members are human IgSF members.

Embodiment 160

In some further embodiments of any one of embodiments 125-159, the mammalian IgSF members are at least two of: CD80, CD86, CD274, PDCD1LG2, ICOSLG, CD276, VTCN1, CD28, CTLA4, PDCD1, ICOS, BTLA, CD4, CD8A, CD8B, LAG3, HAVCR2, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, or CD200R1.

Embodiment 161

In some further embodiments of any one of embodiments 125-160, immunological activity is enhanced.

Embodiment 38

In some further embodiments of any one of embodiments 125-1, immunological activity is suppressed.

Embodiment 162

In some further embodiments of any one of embodiments 125-161, one of the two mammalian cells is a tumor cell.

Embodiment 163

In some further embodiments of any one of embodiments 125-162, the lymphocyte is an NK cell or a T-cell.

Embodiment 164

In some further embodiments of any one of embodiments 125-163, the mammalian cells are a mouse, rat, cynomologus monkey, or human cells.

Embodiment 165

In some further embodiments of any one of embodiments 125-164, at least one of the two affinity modified IgSF domains has between 10% and 90% of the binding affinity of the wild-type IgSF domain to at least one of the cell surface molecular species.

Embodiment 166

In some further embodiments of any one of embodiments 125-165, at least one of the two affinity modified IgSF domains specifically binds to exactly one cell surface molecular species.

Embodiment 167

In some further embodiments of any one of embodiments 125-166, at least one of the two affinity modified IgSF domains has at least 120% of the binding affinity as its wild-type IgSF domain to at least one of the two cell surface molecular species.

Embodiment 168

In some further embodiments of any one of embodiments 125-167, the affinity modified IgSF domains are at least one of an IgV, IgC1, or IgC2 domain.

Embodiment 169

In some further embodiments of any one of embodiments 125-168, each of the at least two affinity modified IgSF domains differs by at least one and no more than ten amino acid substitutions from its wild-type IgSF domain.

Embodiment 170

In some further embodiments of any one of embodiments 125-169, each of the at least two affinity modified IgSF domains differs by at least one and no more than five amino acid substitutions from its wild-type IgSF domain.

Embodiment 171

In some further embodiments of any one of embodiments 125-170, the immunomodulatory protein is covalently bonded, directly or indirectly, to an antibody fragment crystallizable (Fc).

Embodiment 172

In some further embodiments of any one of embodiments 125-171, the immunomodulatory protein is in a pharmaceutically acceptable carrier.

Embodiment 173

In some further embodiments of any one of embodiments 125-172, the protein is glycosylated or pegylated.

Embodiment 174

In some further embodiments of any one of embodiments 125-173, the protein is soluble.

Embodiment 175

In some further embodiments of any one of embodiments 125-174, the protein is bonded to a liposomal membrane.

Embodiment 176

In some further embodiments of any one of embodiments 125-175, the protein is dimerized by intermolecular disulfide bonds.

Embodiment 177

In some further embodiments of any one of embodiments 125-176, the cell surface molecular species are expressed in cis configuration or trans configuration.

Embodiment 178

In some further embodiments of any one of embodiments 125-177, the immunomodulatory protein has at least 85% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-26, a combination, or a fragment thereof.

Embodiment 179

In some further embodiments of any one of embodiments 125-178, the immunomodulatory protein has at least 90% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-26, a combination, or a fragment thereof.

Embodiment 180

In some further embodiments of any one of embodiments 125-179, the immunomodulatory protein has at least 95% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-26, a combination, or a fragment thereof.

Embodiment 181

In some further embodiments of any one of embodiments 125-180, the immunomodulatory protein has at least 99% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-26, a combination, or a fragment thereof.

Embodiment 182

In some further embodiments of any one of embodiments 125-181, the immunomodulatory protein further comprises a second immunomodulatory protein, wherein the second immunomodulatory protein has at least 85% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-26 or a fragment thereof.

Embodiment 183

In some further embodiments of any one of embodiments 125-182, the immunomodulatory protein further comprises a second immunomodulatory protein, wherein the second immunomodulatory protein has at least 90% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-26 or a fragment thereof.

Embodiment 184

In some further embodiments of any one of embodiments 125-183, the immunomodulatory protein further comprises a second immunomodulatory protein, wherein the second immunomodulatory protein has at least 95% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-26 or a fragment thereof.

Embodiment 185

In some further embodiments of any one of embodiments 125-184, the immunomodulatory protein further comprises a second immunomodulatory protein, wherein the second immunomodulatory protein has at least 99% sequence identity with an amino acid sequence selected from SEQ ID NOS: 1-26 or a fragment thereof.

Embodiment 186

In some embodiments, there is provided a recombinant nucleic acid encoding any one of the immunomodulatory proteins of embodiments 125-185.

Embodiment 187

In some embodiments, there is provided a recombinant expression vector comprising a nucleic acid of embodiment 186.

Embodiment 188

In some embodiments, there is provided a recombinant host cell comprising the expression vector of embodiment 187.

Embodiment 189

In some embodiments, there is provided a method of making an immunomodulatory protein of any one of embodiments 125-185, comprising culturing the recombinant host cell under immunomodulatory protein expressing conditions, expressing the immunomodulatory protein encoded by the recombinant expression vector therein, and purifying the recombinant immunomodulatory protein expressed thereby.

Embodiment 190

In some embodiments, there is provided a method of treating a mammalian patient in need of an enhanced or suppressed immunological response by administering a therapeutically effective amount of immunomodulatory protein of any one of embodiments 125-185.

Embodiment 191

In some further embodiments of embodiment 190, the enhanced immunological response treats melanoma, lung cancer, bladder cancer, or a hematological malignancy in the patient.

Embodiment 192

In some further embodiments of embodiment 190, the suppressed immunological response treats Crohn's disease, ulcerative colitis, multiple sclerosis, asthma, rheumatoid arthritis, or psoriasis in the patient.

VIII. Examples

The following examples are included for illustrative purposes only and are not intended to limit the scope of the invention.

Examples 1-8 describe the design, creation, and screening of affinity modified CD80 (B7-1), CD86 (B7-2), ICOSL, and NKp30 immunomodulatory proteins, which are components of the immune synapse (IS) that have a demonstrated dual role in both immune activation and inhibition. These examples demonstrate that affinity modification of IgSF domains yields proteins that can act to both increase and decrease immunological activity. This work also describes the various combinations of those domains fused in pairs (i.e., stacked) to form a Type II immunomodulatory protein to achieve immunomodulatory activity.

Example 1 Generation of Mutant DNA Constructs of IgSF Domains

Example 1 describes the generation of mutant DNA constructs of human CD80, CD86, ICOSL, and NKp30 IgSF domains for translation and expression on the surface of yeast as yeast display libraries.

A. Degenerate Libraries

For libraries that target specific residues of target protein for complete or partial randomization with degenerate codons, the coding DNA's for the extracellular domains (ECD) of human CD80 (SEQ ID NO:28), ICOSL (SEQ ID NO:32), and NKp30 (SEQ ID NO:54) were ordered from Integrated DNA Technologies (Coralville, Iowa) as a set of overlapping oligonucleotides of up to 80 base pairs (bp) in length. To generate a library of diverse variants of each ECD, the oligonucleotides contained desired degenerate codons at desired amino acid positions. Degenerate codons were generated using an algorithm at the URL: rosettadesign.med.unc.edu/SwiftLib/.

In general, positions to mutate and degenerate codons were chosen as follows: crystal structures (CD80, NKp30) or homology models (ICOSL) of the target-ligand pairs of interest were used to identify ligand contact residues as well as residues that are at the protein interaction interface. This analysis was performed using a structure viewer available at the URL:spdbv.vital-it.ch). For example, a crystal structure for CD80 bound to CTLA4 is publicly available at the URL:www.rcsb.org/pdb/explore/explore.do?structureld=1I8L) and a targeted library was designed based on the CD80::CTLA4 interface for selection of improved binders to CTLA4. However, there are no CD80 structures available with ligands CD28 and PDL1, so the same library was also used to select for binders of CD28 (binds the same region on CD80 as CTLA4) and PDL1 (not known if PDL1 binds the same site as CTLA4).

The next step in library design was the alignment of human, mouse, rat and monkey CD80, ICOSL or NKp30 sequences to identify conserved residues. Based on this analysis, conserved target residues were mutated with degenerate codons that only specified conservative amino acid changes plus the wild-type residue. Residues that were not conserved, were mutated more aggressively, but also including the wild-type residue. Degenerate codons that also encoded the wild-type residue were deployed to avoid excessive mutagenesis of target protein. For the same reason, only up to 20 positions were targeted for mutagenesis at a time. These residues were a combination of contact residues and non-contact interface residues.

The oligonucleotides were dissolved in sterile water, mixed in equimolar ratios, heated to 95° C. for five minutes and slowly cooled to room temperature for annealing. ECD-specific oligonucleotide primers that anneal to the start and end of the ECDs, respectively, were then used to generate PCR product. ECD-specific oligonucleotides which overlap by 40-50 bp with a modified version of pBYDS03 cloning vector (Life Technologies USA), beyond and including the BamH1 and Kpn1 cloning sites, were then used to amplify 100 ng of PCR product from the prior step to generate a total of 5 μg of DNA. Both PCR's were by polymerase chain reaction (PCR) using OneTaq 2×PCR master mix (New England Biolabs, USA). The second PCR products were purified using a PCR purification kit (Qiagen, Germany) and resuspended in sterile deionized water.

To prepare for library insertion, a modified yeast display version of vector pBYDS03 was digested with BamH1 and Kpn1 restriction enzymes (New England Biolabs, USA) and the large vector fragment was gel-purified and dissolved in sterile, deionized water. Electroporation-ready DNA for the next step was generated by mixing 12 μg of library DNA with 4 μg of linearized vector in a total volume of 50 μl deionized and sterile water. An alternative way to generate targeted libraries, was to carry out site-directed mutagenesis (Multisite kit, Agilent, USA) of target ECD's with oligonucleotides containing degenerate codons. This approach was used to generate sublibraries that only target specific stretches of target protein for mutagenesis. In these cases, sublibraries were mixed before proceeding to the selection steps. In general, library sizes were in the range of 10E7 to 10E8 clones, except that sublibraries were only in the range of 10E4 to 10E5. Large libraries were generated for CD80, ICOSL, CD86 and NKp30. Sublibraries were generated for CD80, ICOSL and NKp30.

B. Random Libraries

Random libraries were also constructed to identify variants of the ECD of CD80 (SEQ ID NO:28), CD86 (SEQ ID NO: 29), ICOSL (SEQ ID NO:32) and NKp30 (SEQ ID NO:54. DNA encoding wild-type ECDs was cloned between the BamH1 and Kpn1 sites of modified yeast display vector pBYDS03 and then released using the same restriction enzymes. The released DNA was then mutagenized with the Genemorph II kit (Agilent, USA) so as to generate an average of three to five amino acid changes per library variant. Mutagenized DNA was then amplified by the two-step PCR and further processed as described above for targeted libraries.

Example 2 Introduction of DNA Libraries into Yeast

Example 2 describes the introduction of CD80, CD86, ICOSL, and NKp30 DNA libraries into yeast.

To introduce degenerate and random library DNA into yeast, electroporation-competent cells of yeast strain BJ5464 (ATCC.org; ATCC number 208288) were prepared and electroporated on a Gene Pulser II (Biorad, USA) with the electroporation-ready DNA from the step above essentially as described (Colby, D. W. et al. 2004 Methods Enzymology 388, 348-358). The only exception is that transformed cells were grown in non-inducing minimal selective SCD-Leu medium to accommodate the LEU2 selective marker carried by modified plasmid pBYDS03.

Library size was determined by plating dilutions of freshly recovered cells on SCD-Leu agar plates and then extrapolating library size from the number of single colonies from plating that generated at least 50 colonies per plate. The remainder of the electroporated culture was grown to saturation and cells from this culture were subcultured into the same medium once more to minimize the fraction of untransformed cells. To maintain library diversity, this subculturing step was carried out using an inoculum that contained at least 10× more cells than the calculated library size. Cells from the second saturated culture were resuspended in fresh medium containing sterile 25% (weight/volume) glycerol to a density of 10E10/ml and frozen and stored at −80° C. (frozen library stock).

One liter of SCD-Leu media consists of 14.7 grams of sodium citrate, 4.29 grams of citric acid monohydrate, 20 grams of dextrose, 6.7 grams of Difco brand yeast nitrogen base, and 1.6 grams yeast synthetic drop-out media supplement without leucine. Media was filtered sterilized before use using a 0.2 μM vacuum filter device.

Library size was determined by plating dilutions of freshly recovered cells on SCD-Leu agar plates and then extrapolating library size from the number of single colonies from a plating that generate at least 50 colonies per plate.

To segregate plasmid from cells that contain two or more different library clones, a number of cells corresponding to 10 times the library size, were taken from the overnight SCD-Leu culture and subcultured 1/100 into fresh SCD-Leu medium and grown overnight. Cells from this overnight culture were resuspended in sterile 25% (weight/volume) glycerol to a density of 10E10/ml and frozen and stored at −80° C. (frozen library stock).

Example 3 Yeast Selection

Example 3 describes the selection of yeast expressing affinity modified variants of CD80, CD86, ICOSL, and NKp30.

A number of cells equal to at least 10 times the library size were thawed from individual library stocks, suspended to 0.1×10E6 cells/ml in non-inducing SCD-Leu medium, and grown overnight. The next day, a number of cells equal to 10 times the library size were centrifuged at 2000 RPM for two minutes and resuspended to 0.5×10E6 cells/ml in inducing SCDG-Leu media. One liter of the SCDG-Leu induction media consists of 5.4 grams Na₂HPO₄, 8.56 grams of NaH₂PO₄*H₂0, 20 grams galactose, 2.0 grams dextrose, 6.7 grams Difco yeast nitrogen base, and 1.6 grams of yeast synthetic drop out media supplement without leucine dissolved in water and sterilized through a 0.22 μm membrane filter device. The culture was grown for two days at 20° C. to induce expression of library proteins on the yeast cell surface.

Cells were processed with magnetic beads to reduce non-binders and enrich for all CD80, CD86, ICOSL or NKp30 variants with the ability to bind their exogenous recombinant counter-structure proteins. For example, yeast displayed targeted or random CD80 libraries were selected against each of CD28, CTL-4, PD-L1, ICOS, and B7-H6 separately. This was then followed by two to three rounds of flow cytometry sorting using exogenous counter-structure protein staining to enrich the fraction of yeast cells that displays improved binders. Magnetic bead enrichment and selections by flow cytometry are essentially as described in Keith D. Miller,1 Noah B. Pefaur,2 and Cheryl L. Baird1 Current Protocols in Cytometry 4.7.1-4.7.30, July 2008.

With CD80, CD86, ICOSL, and NKp30 libraries, target ligand proteins were sourced from R&D Systems (USA) as follows: human rCD28.Fc (i.e., recombinant CD28-Fc fusion protein), rPDL1.Fc, rCTLA4.Fc, rICOS.Fc, and rB7H6.Fc. Magnetic streptavidin beads were obtained from New England Biolabs, USA. For biotinylation of counter-structure protein, biotinylation kit cat#21955, Life Technologies, USA, was used. For two-color, flow cytometric sorting, a Becton Dickinson FACS Aria II sorter was used. CD80, CD86, ICOSL, or NKp30 display levels were monitored with an anti-hemagglutinin antibody labeled with Alexafluor 488 (Life Technologies, USA). Ligand binding Fc fusion proteins rCD28.Fc, rCTLA4.Fc, rPDL1.Fc, rICOS.Fc, or rB7-H6.Fc were detected with PE conjugated human Ig specific goat Fab (Jackson ImmunoResearch, USA). Doublet yeast were gated out using forward scatter (FSC)/side scatter (SSC) parameters, and sort gates were based upon higher ligand binding detected in FL4 that possessed more limited tag expression binding in FL1.

Yeast outputs from the flow cytometric sorts were assayed for higher specific binding affinity. Sort output yeast were expanded and re-induced to express the particular IgSF affinity modified domain variants they encode. This population then can be compared to the parental, wild-type yeast strain, or any other selected outputs, such as the bead output yeast population, by flow cytometry.

For ICOSL, the second sort outputs (F2) were compared to parental ICOSL yeast for binding of each rICOS.Fc, rCD28.Fc, and rCTLA4.Fc by double staining each population with anti-HA (hemagglutinin) tag expression and the anti-human Fc secondary to detect ligand binding.

In the case of ICOSL yeast variants selected for binding to ICOS, the F2 sort outputs gave Mean Fluorescence Intensity (MFI) values of 997, when stained with 5.6 nM rICOS.Fc, whereas the parental ICOSL strain MFI was measured at 397 when stained with the same concentration of rICOS.Fc. This represents a roughly three-fold improvement of the average binding in this F2 selected pool of clones, and it is predicted that individual clones from that pool will have much better improved MFI/affinity when individually tested.

In the case of ICOSL yeast variants selected for binding to CD28, the F2 sort outputs gave MFI values of 640 when stained with 100 nM rCD28.Fc, whereas the parental ICOSL strain MFI was measured at 29 when stained with the same concentration of rCD28.Fc (22-fold improvement). In the case of ICOSL yeast variants selected for binding to CTLA4, the F2 sort outputs gave MFI values of 949 when stained with 100 nM rCTLA4.Fc, whereas the parental ICOSL strain MFI was measured at 29 when stained with the same concentration of rCTLA4.Fc (32-fold improvement).

In the case of NKp30 yeast variants selected for binding to B7-H6, the F2 sort outputs gave MFI values of 533 when stained with 16.6 nM rB7H6.Fc, whereas the parental NKp30 strain MFI was measured at 90 when stained with the same concentration of rB7H6.Fc (6-fold improvement).

Importantly, the MFIs of all F2 outputs described above when measured with the anti-HA tag antibody on FL1 did not increase and sometimes went down compared to wild-type strains, indicating that increased binding was not a function of increased expression of the selected variants on the surface of yeast, and validated gating strategies of only selecting mid to low expressors with high ligand binding.

Example 4 Reformatting Selection Outputs as Fc-Fusions and in Various Immunomodulatory Protein Types

Example 4 describes reformatting of selection outputs as immunomodulatory proteins containing an affinity modified (variant) extracellular domain (ECD) of CD80 or ICOSL, fused to an Fc molecule (variant ECD-Fc fusion molecules).

Output cells from final flow cytometric CD80 and ICOSL sorts were grown to terminal density in SCD-Leu medium. Plasmid DNA's from each output were isolated using a yeast plasmid DNA isolation kit (Zymoresearch, USA). For Fc fusions, PCR primers with added restriction sites suitable for cloning into the Fc fusion vector of choice were used to batch-amplify from the plasmid DNA preps the coding DNA's for the mutant target ECD's. After restriction digestion, the PCR products were ligated into an appropriate Fc fusion vector followed by chemical transformation into strain XL1 Blue E. Coli (Agilent, USA) or NEB5alpha (New England Biolabs) as directed by supplier. Exemplary of an Fc fusion vector is pFUSE-hIgG1-Fc2 (Invivogen, USA).

Dilutions of transformation reactions were plated on LB-agar containing 100 μg/ml carbenicillin (Teknova, USA) to generate single colonies. Up to 96 colonies from each transformation were then grown in 96 well plates to saturation overnight at 37 C in LB-broth (Teknova cat # L8112) and a small aliquot from each well was submitted for DNA sequencing of the ECD insert in order to identify the mutation(s) in all clones. Sample preparation for DNA sequencing was carried out using protocols provided by the service provider (Genewiz; South Plainfield, N.J.). After removal of sample for DNA sequencing, glycerol was then added to the remaining cultures for a final glycerol content of 25% and plates were stored at −20° C. for future use as master plates (see below). Alternatively, samples for DNA sequencing were generated by replica plating from grown liquid cultures to solid agar plates using a disposable 96 well replicator (VWR, USA). These plates were incubated overnight to generate growth patches and the plates were submitted to Genewiz as specified by Genewiz.

After identification of clones of interest from analysis of Genewiz-generated DNA sequencing data, clones of interest were recovered from master plates and individually grown to density in 5 ml liquid LB-broth containing 100 μg/ml carbenicillin (Teknova, USA) and 2 ml of each culture were then used for preparation of approximately 10 μg of miniprep plasmid DNA of each clone using a standard kit such as the Pureyield kit (Promega). Identification of clones of interest generally involved the following steps. First, DNA sequence data files were downloaded from the Genewiz website. All sequences were then manually curated so that they start at the beginning of the ECD coding region. The curated sequences were then batch-translated using a suitable program available at the URL: www.ebi.ac.uk/Tools/st/emboss transeq/. The translated sequences were then aligned using a suitable program available at the URL:multalin.toulouse.inra.fr/multalin/multalin.html.

Clones of interest were then identified using the following criteria: 1.) identical clone occurs at least two times in the alignment and 2.) a mutation occurs at least two times in the alignment and preferably in distinct clones. Clones that meet at least one of these criteria were clones that have been enriched by our sorting process due to improved binding.

To generate immunomodulatory proteins containing an ECD of CD80 or ICOSL with at least one affinity-modified domain, the encoding nucleic acid molecule was generated to encode a protein designed as follows: signal peptide followed by variant (mutant) ECD followed by a linker of three alanines (AAA) followed by a human IgG1 Fc containing the mutation N82G with reference to wild-type human IgG1 Fc set forth in SEQ ID NO: 226. Since the construct does not include any antibody light chains that can form a covalent bond with a cysteine, the human IgG1 Fc also contains replacement of the cysteine residues to a serine residue at position 5 (C5S) compared to the wild-type or unmodified Fc set forth in SEQ ID NO: 226.

In addition, Example 8 below describes further immunomodulatory proteins that were generated as stack constructs containing at least two different affinity modified domains from identified variant CD80, CD86, ICOSL, and NKp30 molecules linked together and fused to an Fc.

Example 5 Expression and Purification of Fc-Fusions

Example 5 describes the high throughput expression and purification of Fc-fusion proteins containing variant ECD CD80, CD86, ICOSL, and Nkp30.

Recombinant variant Fc fusion proteins were produced with Expi293 expression system (Invitrogen, USA). 4 μg of each plasmid DNA from the previous step was added to 200 μl Opti-MEM (Invitrogen, USA) at the same time as 10.8 μl ExpiFectamine was separately added to another 200 μl Opti-MEM. After 5 minutes, the 200 μl of plasmid DNA was mixed with the 200 μl of ExpiFectamine and was further incubated for an additional 20 minutes before adding this mixture to cells. Ten million Expi293 cells were dispensed into separate wells of a sterile 10 ml, conical bottom, deep 24 well growth plate (Thomson Instrument Company, USA) in a volume 3.4 ml Expi293 media (Invitrogen, USA). Plates were shaken for 5 days at 120 RPM in a mammalian cell culture incubator set to 95% humidity and 8% CO₂. Following a 5 day incubation, cells were pelleted and culture supernatants were removed.

Protein was purified from supernatants using a high throughput 96 well Protein A purification kit using the manufacturer's protocol (Catalog number 45202, Life Technologies, USA). Resulting elution fractions were buffer exchanged into PBS using Zeba 96 well spin desalting plate (Catalog number 89807, Life Technologies, USA) using the manufacturer's protocol. Purified protein was quantitated using 280 nm absorbance measured by Nanodrop instrument (Thermo Fisher Scientific, USA), and protein purity was assessed by loading 5 μg of protein on NUPAGE pre-cast, polyacrylamide gels (Life Technologies, USA) under denaturing and reducing conditions and subsequent gel electrophoresis. Proteins were visualized in gel using standard Coomassie staining.

Example 6 Assessment of Binding and Activity of Affinity-Matured IgSF Domain-Containing Molecules

A. Binding to Cell-Expressed Counter Structures

This Example describes Fc-fusion binding studies to show specificity and affinity of CD80 and ICOSL domain variant immunomodulatory proteins for cognate binding partners.

To produce cells expressing cognate binding partners, full-length mammalian surface expression constructs for each of human CD28, CTLA4, PD-L1, ICOS, and B7-H6 were designed in pcDNA3.1 expression vector (Life Technologies) and sourced from Genscript, USA. Binding studies were carried out using the Expi293F transient transfection system (Life Technologies, USA) described above. The number of cells needed for the experiment was determined, and the appropriate 30 ml scale of transfection was performed using the manufacturer's suggested protocol. For each CD28, CTLA-4, PD-L1, ICOS, B7-H6 or mock 30 ml transfection, 75 million Expi293F cells were incubated with 30 μg expression construct DNA and 1.5 ml diluted ExpiFectamine 293 reagent for 48 hours, at which point cells were harvested for staining.

For staining by flow cytometry, 200,000 cells of appropriate transient transfection or negative control were plated in 96 well round bottom plates. Cells were spun down and resuspended in staining buffer (PBS (phosphate buffered saline), 1% BSA (bovine serum albumin), and 0.1% sodium azide) for 20 minutes to block non-specific binding. Afterwards, cells were centrifuged again and resuspended in staining buffer containing 100 nM to 1 nM variant immunomodulatory protein, depending on the experiment of each candidate CD80 variant Fc, ICOSL variant Fc, or stacked IgSF variant Fc fusion protein in 50 μl. Primary staining was performed on ice for 45 minutes, before washing cells in staining buffer twice. PE-conjugated anti-human Fc (Jackson ImmunoResearch, USA) was diluted 1:150 in 50 μl staining buffer and added to cells and incubated another 30 minutes on ice. Secondary antibody was washed out twice, cells were fixed in 4% formaldehyde/PBS, and samples were analyzed on FACScan flow cytometer (Becton Dickinson, USA).

Mean Fluorescence Intensity (MFI) was calculated for each transfectant and negative parental line with Cell Quest Pro software (Becton Dickinson, USA).

B. Bioactivity Characterization

This Example further describes Fc-fusion variant protein bioactivity characterization in human primary T cell in vitro assays.

1. Mixed Lymphocyte Reaction (MLR)

Soluble rICOSL.Fc or rCD80.Fc bioactivity was tested in a human Mixed Lymphocyte Reaction (MLR). Human primary dendritic cells (DC) were generated by culturing monocytes isolated from PBMC (BenTech Bio, USA) in vitro for 7 days with 500 U/ml rIL-4 (R&D Systems, USA) and 250 U/ml rGM-CSF (R&D Systems, USA) in Ex-Vivo 15 media (Lonza, Switzerland). 10,000 matured DC and 100,000 purified allogeneic CD4+ T cells (BenTech Bio, USA) were co-cultured with ICOSL or CD80 variant Fc fusion proteins and controls in 96 well round bottom plates in 200 μl final volume of Ex-Vivo 15 media. On day 5, IFN-gamma secretion in culture supernatants was analyzed using the Human IFN-gamma Duoset ELISA kit (R&D Systems, USA). Optical density was measured by VMax ELISA Microplate Reader (Molecular Devices, USA) and quantitated against titrated rIFN-gamma standard included in the IFN-gamma Duo-set kit (R&D Systems, USA).

2. Anti-CD3 Coimmobilization Assay

Costimulatory bioactivity of ICOSL and CD80 Fc fusion variants was determined in anti-CD3 coimmobilization assays. 1 nM or 4 nM mouse anti-human CD3 (OKT3, Biolegends, USA) was diluted in PBS with 1 nM to 80 nM rICOSL.Fc or rCD80.Fc variant proteins. This mixture was added to tissue culture treated flat bottom 96 well plates (Corning, USA) overnight to facilitate adherence of the stimulatory proteins to the wells of the plate. The next day, unbound protein was washed off the plates and 100,000 purified human pan T cells (BenTech Bio, US) or human T cell clone BC3 (Astarte Biologics, USA) were added to each well in a final volume of 200 μl of Ex-Vivo 15 media (Lonza, Switzerland). Cells were cultured 3 days before harvesting culture supernatants and measuring human IFN-gamma levels with Duoset ELISA kit (R&D Systems, USA) as mentioned above.

C. Results

Results for the binding and activity studies for exemplary tested variants are shown in Tables 6-8. In particular, Table 6 indicates exemplary IgSF domain amino acid substitutions (replacements) in the ECD of CD80 selected in the screen for affinity-maturation against the respective cognate structure CD28. Table 7 indicates exemplary IgSF domain amino acid substitutions (replacements) in the ECD of CD80 selected in the screen for affinity-maturation against the respective cognate structure PD-L1. Table 8 indicates exemplary IgSF domain amino acid substitutions (replacements) in the ECD of ICOSL selected in the screen for affinity-maturation against the respective cognate structures ICOS and CD28. For each Table, the exemplary amino acid substitutions are designated by amino acid position number corresponding to the respective reference unmodified ECD sequence as follows. For example, the reference unmodified ECD sequence in Tables 6 and 7 is the unmodified CD80 ECD sequence set forth in SEQ ID NO:28 and the reference unmodified ECD sequence in Table 8 is the unmodified ICOSL ECD sequence (SEQ ID NO:32). The amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed after the number. Column 2 sets forth the SEQ ID NO identifier for the variant ECD for each variant ECD-Fc fusion molecule.

Also shown is the binding activity as measured by the Mean Fluorescence Intensity (MFI) value for binding of each variant Fc-fusion molecule to cells engineered to express the cognate counter structure ligand and the ratio of the MFI compared to the binding of the corresponding unmodified ECD-Fc fusion molecule not containing the amino acid substitution(s) to the same cell-expressed counter structure ligand. The functional activity of the variant Fc-fusion molecules to modulate the activity of T cells also is shown based on the calculated levels of IFN-gamma in culture supernatants (pg/ml) generated either i) with the indicated variant ECD-Fc fusion molecule coimmoblized with anti-CD3 or ii) with the indicated variant ECD-Fc fusion molecule in an MLR assay. The Tables also depict the ratio of IFN-gamma produced by each variant ECD-Fc compared to the corresponding unmodified ECD-Fc in both functional assays.

As shown, the selections resulted in the identification of a number of CD80 or ICOSL IgSF domain variants that were affinity-modified to exhibit increased binding for at least one, and in some cases more than one, cognate counter structure ligand. In addition, the results showed that affinity modification of the variant molecules also exhibited improved activities to both increase and decrease immunological activity depending on the format of the molecule. For example, coimmobilization of the ligand likely provides a multivalent interaction with the cell to cluster or increase the avidity to favor agonist activity and increase T cell activation compared to the unmodified (e.g. wildtype) ECD-Fc molecule not containing the amino acid replacement(s). However, when the molecule is provided as a bivalent Fc molecule in solution, the same IgSF domain variants exhibited an antagonist activity to decrease T cell activation compared to the unmodified (e.g. wildtype) ECD-Fv molecule not containing the amino acid replacement(s).

TABLE 6 CD80 variants selected against CD28. Molecule sequences, binding data, and costimulatory bioactivity data. Coimmobili- zation with Binding anti-CD3 MLR CD28 CTLA-4 PD-L1 IFN-gamma IFN-gamma SEQ ID MFI MFI MFI pg/ml levels pg/ml NO (parental (parental (parental (parental (parental CD80 mutation(s) (ECD) ratio) ratio) ratio) ratio) ratio) L70Q/A91G 55 125 283 6 93 716 (1.31) (1.36) (0.08) (1.12) (0.83) L70Q/A91G/T130A 56 96 234 7 99 752 (1.01) (1.13) (0.10) (1.19) (0.87) L70Q/A91G/I118A/ 57 123 226 7 86 741 T120S/T130A (1.29) (1.09) (0.10) (1.03) (0.86) V4M/L70Q/A91G/ 58 89 263 6 139 991 T120S/T130A (0.94) (1.26) (0.09) (1.67) (1.14) L70Q/A91G/T120S/ 59 106 263 6 104 741 T130A (1.12) (1.26) (0.09) (1.25) (0.86) V20L/L70Q/A91S/ 60 105 200 9 195 710 T120S/T130A (1.11) (0.96) (0.13) (2.34) (0.82) S44P/L70Q/A91G/ 61 88 134 5 142 854 T130A (0.92) (0.64) (0.07) (1.71) (0.99) L70Q/A91G/E117G/ 62 120 193 6 98 736 T120S/T130A (1.27) (0.93) (0.08) (1.05) (0.85) A91G/T120S/ 63 84 231 44 276 714 T130A (0.89) (1.11) (0.62) (3.33) (0.82) L70R/A91G/T120S/ 64 125 227 6 105 702 T130A (1.32) (1.09) (0.09) (1.26) (0.81) L70Q/E81A/A91G/ 65 140 185 18 98 772 T120S/I127T/ (1.48) (0.89) (0.25) (1.18) (0.89) T130A L70Q/Y87N/A91G/ 66 108 181 6 136 769 T130A (1.13) (0.87) (0.08) (1.63) (0.89) T28S/L70Q/A91G/ 67 32 65 6 120 834 E95K/T120S/T130A (0.34) (0.31) (0.08) (1.44) (0.96) N63S/L70Q/A91G/ 68 124 165 6 116 705 T120S/T130A (1.30) (0.79) (0.08) (1.39) (0.81) K36E/I67T/L70Q/ 69 8 21 5 53 852 A91G/T120S/ (0.09) (0.10) (0.08) (0.63) (0.98) T130A/N152T E52G/L70Q/A91G/ 70 113 245 6 94 874 T120S/T130A (1.19) (1.18) (0.08) (1.13) (1.01) K37E/F59S/L70Q/ 71 20 74 6 109 863 A91G/T120S/ (0.21) (0.36) (0.08) (1.31) (1.00) T130A A91G/S103P 72 39 56 9 124 670 (0.41) (0.27) (0.13) (1.49) (0.77) K89E/T130A 73 90 148 75 204 761 (0.95) (0.71) (1.07) (2.45) (0.88) A91G 74 96 200 85 220 877 (1.01) (0.96) (1.21) (2.65) (1.01) D60V/A91G/T120S/ 75 111 222 12 120 744 T130A (1.17) (1.07) (0.18) (1.44) (0.86) K54M/A91G/T120S 76 68 131 5 152 685 (0.71) (0.63) (0.08) (1.83) (0.79) M38T/L70Q/E77G/ 77 61 102 5 119 796 A91G/T120S/ (0.64) (0.49) (0.07) (1.43) (0.92) T130A/N152T R29H/E52G/L70R/ 78 100 119 5 200 740 E88G/A91G/T130A (1.05) (0.57) (0.08) (2.41) (0.85) Y31H/T41G/L70Q/ 79 85 85 6 288 782 A91G/T120S/ (0.89) (0.41) (0.08) (3.47) (0.90) T130A V68A/110A 80 103 233 48 163 861 (1.08) (1.12) (0.68) (1,96) (0.99) S66H/D90G/T110A/ 81 33 121 11 129 758 F116L (0.35) (0.58) (0.15) (1.55) (0.88) R29H/E52G/T120S/ 82 66 141 11 124 800 T130A (0.69) (0.68) (0.15) (1.49) (0.92) A91G/L102S 83 6 6 5 75 698 (0.06) (0.03) (0.08) (0.90) (0.81) I67T/L70Q/A91G/ 84 98 160 5 1751 794 T120S (1.03) (0.77) (0.08) (21.1) (0.92) L70Q/A91G/T110A/ 85 8 14 5 77 656 T120S/T130A (0.09) (0.07) (0.07) (0.93) (0.76) M38V/T41D/M43I/ 86 5 8 8 82 671 W50G/D76G/V83A/ (0.06) (0.04) (0.11) (0.99) (0.78) K89E/T120S/T130A V22A/L70Q/S121P 87 5 7 5 105 976 (0.06) (0.04) (0.07) (1.27) (1.13) A12V/S15F/Y31H/ 88 6 6 5 104 711 T41G/T130A/P137L/ (0.06) (0.03) (0.08) (1.25) (0.82) N152T I67F/L70R/E88G/ 89 5 6 6 62 1003 A91G/T120S/T130A (0.05) (0.03) (0.08) (0.74) (1.16) E24G/L25P/L70Q/ 90 26 38 8 101 969 T120S (0.27) (0.18) (0.11) (1.21) (1.12) A91G/F92L/F108L/ 91 50 128 16 59 665 T120S (0.53) (0.61) (0.11) (0.71) (0.77) WT CD80 28 95 208 70 83 866 (1.00) (1.00) (1.00) (1.00) (1.00)

TABLE 7 CD80 variants selected against PD-Li. Molecule sequences, binding data, and costimulatory bioactivity data. Coimmobilization Binding with anti-CD3 MLR SEQ CD28 CTLA-4 PD-L1 IFN-gamma IFN-gamma ID MFI MFI MFI pg/ml levels pg/ml NO (parental (parental (parental (parental (parental CD80 mutation(s) (ECD) ratio) ratio) ratio) ratio) ratio) R29D/Y31L/Q33H/ 92 1071 1089 37245 387 5028 K36G/M38I/T41A/ (0.08) (0.02) (2.09) (0.76) (0.26) M43R/M47T/E81V/ L85R/K89N/A91T/ F92P/K93V/R94L/ I118T/N149S R29D/Y31L/Q33H/ 93 1065 956 30713 400 7943 K36G/M38I/T41A/ (0.08) (0.02) (1.72) (0.79) (0.41) M43R/M47T/E81V/ L85R/K89N/A91T/ F92P/K93V/R94L/ N144S/N149S R29D/Y31L/Q33H/ 94 926 954 47072 464 17387 K36G/M38I/T41A/ (0.07) (0.02) (2.64) (0.91) (0.91) M42T/M43R/M47T/ E81V/L85R/K89N/ A91T/F92P/K93V/ R94L/L148S/N149S E24G/R29D/Y31L/ 95 1074 1022 1121 406 13146 Q33H/K36G/M38I/ (0.08) (0.02) (0.06) (0.80) (0.69) T41A/M43R/M47T/ F59L/E81V/L85R/ K89N/A91T/F92P/ K93V/R94L/H96R R29D/Y31L/Q33H/ 96 1018 974 25434 405 24029 K36G/M38I/T41A/ (0.08) (0.02) (1.43) (0.80) (1.25) M43R/M47T/E81V/ L85R/K89N/A91T/ F92P/K93V/R94L/ N149S R29V/M43Q/E81R/ 97 1029 996 1575 342 11695 L85I/K89R/D9OL/ (0.08) (0.02) (0.09) (0.67) (0.61) A91E/F92N/K93Q/ R94G T41I/A91G 98 17890 50624 12562 433 26052 (1.35) (1.01) (0.70) (0.85) (1.36) K89R/D90K/A91G/ 99 41687 49429 20140 773 6345 F92Y/K93R/N122S/ (3.15) (0.99) (1.13) (1.52) (0.33) N178S K89R/D90K/A91G/ 100 51663 72214 26405 1125 9356 F92Y/K93R (3.91) (1.44) (1.48) (2.21) (0.49) K36G/K37Q/M38I/ 101 1298 1271 3126 507 3095 F59L/E81V/L85R/ (0.10) (0.03) (0.18) (1.00) (0.16) K89N/A91T/F92P/ K93V/R94L/E99G/ T130A/N149S AE88D/K89R/D90K/ 102 31535 50868 29077 944 5922 A91G/F92Y/K93R (2.38) (1.02) (1.63) (1.85) (0.31) K36G/K37Q/M38I/ 103 1170 1405 959 427 811 L40M (0.09) (0.03) (0.05) (0.84) (0.04) K36G 104 29766 58889 20143 699 30558 (2.25) (1.18) (1.13) (1.37) (1.59) WTCD80 28 13224 50101 17846 509 19211 (1.00) (1.00) (1.00) (1.00) (1.00)

TABLE 8 ICOSL variants selected against CD28 or ICOS. Molecule sequences, binding data, and costimulatory bioactivity data. Coimmobilization with anti-CD3 MLR Binding IFN-gamma IFN-gamma SEQ ICOS OD CD28 MFI pg/ml levels pg/ml ICOSL ID NO (parental (parental (parental (parental mutation(s) (ECD) ratio) ratio) ratio) ratio) N52S 109 1.33 162 1334  300 (1.55) (9.00) (1.93)  (0.44) N52H 110 1.30 368 1268   39 (1.51) (20.44) (1.83)  (0.06) N52D 111 1.59 130 1943  190 (1.85) (7.22) (2.80)  (0.28) N52Y/N57Y/ 112 1.02 398 510*  18 F138L/L203P (1.19) (22.11) (1.47*) (0.03) N52H/N57Y/Q100P 113 1.57 447 2199   25 (1.83) (24.83) (3.18)  (0.04) N52S/Y146C/ 114 1.26 39 1647  152 Y152C (1.47) (2.17) (2.38)  (0.22) N52H/C198R 115 1.16 363 744* ND (1.35) (20.17) (2.15*) (ND) N52H/C140D/T225A 116 ND 154 522* ND (ND) (8.56) (1.51*) (ND) N52H/C198R/T225A 117 1.41 344 778*  0 (1.64) (19.11) (2.25*) (0)   N52H/K92R 118 1.48 347 288*  89 (1.72) (19.28) (0.83*) (0.13) N52H/S99G 119 0.09 29 184* 421 (0.10) (1.61) (0.53*) (0.61) N52Y 120 0.08 18 184* 568 (0.09) (1.00) (0.53*) (0.83) N57Y 121 1.40 101 580* 176 (1.63) (5.61) (1.68*) (0.26) N57Y/Q100P 122 0.62 285 301* 177 (0.72) (15.83) (0.87*) (0.26) N52S/S130G/ 123 0.16 24 266* 1617  Y152C (0.19) (1.33) (0.77*) (2.35) N52S/Y152C 124 0.18 29 238* 363 (0.21) (1.61) (0.69*) (0.53) N52S/C198R 125 1.80 82 1427  201 (2.09) (4.56) (2.06)  (0.29) N52Y/N57Y/Y152C 126 0.08 56 377* 439 (0.09) (3.11) (1.09*) (0.64) N52Y/N57Y/ 127 ND 449 1192  ND H129P/C198R (ND) (24.94) (1.72)  (ND) N52H/L161P/ 128 0.18 343 643* 447 C198R (0.21) (19.05) (1.86*) (0.65) N52S/T113E 129 1.51 54 451* 345 (1.76) (3.00) (1.30*) (0.50) S54A 130 1.62 48 386* 771 (1.88) (2.67) (1.12*) (1.12) N52D/S54P 131 1.50 38 476* 227 (1.74) (2.11) (1.38*) (0.33) N52K/L208P 132 1.91 291 1509  137 (2.22) (16.17) (2.18)  (0.20) N52S/Y152H 133 0.85 68 2158  221 (0.99) (3.78) (3.12)  (0.32) N52D/V151A 134 0.90 19 341* 450 (1.05) (1.06) (0.99*) (0.66) N52H/I143T 135 1.83 350 2216  112 (2.13) (19.44) (3.20)  (0.16) N52S/L80P 136 0.09 22 192* 340 (0.10) (1.22) (0.55*) (0.49) F120S/Y152H/N201S 137 0.63 16 351* 712 (0.73) (0.89) (1.01*) (1.04) N52S/R75Q/L203P 138 1.71 12 1996  136 (1.99) (0.67) (2.88)  (0.20) N52S/D158G 139 1.33 39 325* 277 (1.55) (2.17) (0.94*) (0.40) N52D/Q133H 140 1.53 104 365* 178 (1.78) (5.78) (1.05*) (0.26) WT ICOSL 32 0.86 18 692/346* 687 (1.00) (1.00) (1.00)  (1.00) *Parental ratio calculated using 346 pg/ml IFN-gamma for WT ICOSL

Example 7 Ligand Binding Competition Assay

As shown in Example 6, several CD80 variant molecules exhibited improved binding to one or both of CD28 and PD-L1. To further assess the binding activity of CD80 to ligands CD28 and PD-L1, this Example describes a ligand competition assay assessing the non-competitive nature of exemplary CD80 variants to bind both CD28 and PD-L1.

An ELISA based binding assay was set up incorporating plate-bound CD80 variant A91G ECD-Fc to assess the ability of CD80 to simultaneously bind CD28 and PD-L1. Maxisorp 96 well ELISA plates (Nunc, USA) were coated overnight with 100 nM human recombinant CD80 variant A91G ECD-Fc fusion protein in PBS. The following day unbound protein was washed out, and the plate was blocked with 1% bovine serum albumin (Millipore, USA)/PBS for 1 hour at room temperature. This blocking reagent was washed out three times with PBS/0.05% Tween, which included a two minute incubation on a platform shaker for each wash.

In one arm of the competition assay, CD80 was incubated with CD28, and then CD28-bound CD80 was then assessed for competitive binding in the presence of either the other known CD80 ligand counter structures PD-L1 or CTLA-4 or negative control ligand PD-L2. Specifically, biotinylated recombinant human CD28 Fc fusion protein (rCD28.Fc; R&D Systems) was titrated into the wells starting at 10 nM, diluting out for eight points with 1:2 dilutions in 25 μl volume. Immediately after adding the biotinylated rCD28.Fc, unlabeled competitive binders, recombinant human PD-L1 monomeric his-tagged protein, recombinant human CTLA-4 monomeric his-tagged protein, or a negative control human recombinant PD-L2 Fc fusion protein (R&D Systems) were added to wells at 2000/1000/500 nM respectively in 25 al volume for a final volume of 50 μl. These proteins were incubated together for one hour before repeating the three wash steps as described above.

After washing, 2.5 ng per well of HRP-conjugated streptavidin (Jackson Immunoresearch, USA) was diluted in 1% BSA/PBS and added to wells to detect bound biotinylated rCD28.Fc. After one hour incubation, wells were washed again three times as described above. To detect signal, 50 μl of TMB substrate (Pierce, USA) was added to wells following wash and incubated for 7 minutes, before adding 50 ul 2M sulfuric acid stop solution. Optical density was determined on an Emax Plus microplate reader (Molecular Devices, USA). Optical density values were graphed in Prism (Graphpad, USA).

The results are set forth in FIG. 1A. The results showed decreased binding of biotinylated rCD28.Fc to the CD80 variant A91G ECD-Fc fusion protein with titration of the rCD28.Fc. When rCD28.Fc binding was performed in the presence of non-competitive control protein, rPDL2, there was no decrease in CD28 binding for CD80 (solid triangle). In contrast, a competitive control protein, rCTLA-4, when incubated with the CD28.Fc, did result in decreased CD28 binding for CD80 as expected (x line). When recombinant PD-L1 was incubated with CD28.Fc, no decrease in CD28 binding to CD80 was observed, which demonstrated that the epitopes of CD28 and PD-L1 for CD80 are non-competitive. Binding of the recombinant PD-L1 protein used in the CD28 competition assay to CD80 was confirmed by incubating the biotinylated PD-L1 in the presence of non-biotinylated rCD28.Fc (square).

The reverse competition also was set up in which CD80 was incubated with PD-L1, and then PD-L1-bound CD80 was then assessed for competitive binding in the presence of either the other known CD80 ligand counter structures CD28 or CTLA-4 or negative control ligand PD-L2. Specifically, the assay was performed by titrating biotinylated recombinant human PD-L1-his monomeric protein into wells containing the recombinant CD80 variant. Because binding is weaker with this ligand, titrations started at 5000 nM with similar 1:2 dilutions over eight points in 25 μL. When the rPD-L1-his was used to detect binding, the competitive ligands human rCD28.Fc, human rCTLA-4.Fc, or human rPD-L2.Fc control were added at 2.5 nM final concentration in 25 μl for a total volume of 50 μl. The subsequent washes, detection, and OD measurements were the same as described above.

The results are set forth in FIG. 1B. Titrated PD-L1-his binding alone confirmed that PD-L1 bound to the CD80 variant A91G ECD-Fc fusion molecule immobilized on the plate (square). When PD-L1-his binding was performed in the presence of non-competitive control protein, rPDL2, there was no decrease in PD-L1 binding for CD80 (triangle). The CD28-competitive control protein, rCTLA-4, when incubated with the PD-L1-his, did not result in decreased PD-L1 binding for CD80 (x line), even though CTLA-4 is competitive for CD28. This result further demonstrated that lack of competition between CD28 and PD-L1 for CD80 binding. Finally, when PD-L1-his was incubated with CD28.Fc, no decrease in PD-L1 binding to CD80 was observed, which demonstrated that the epitopes of CD28 and PD-L1 for CD80 are non-competitive.

Thus, the results showed that CTLA-4, but not PD-L1 or the negative control PD-L2, competed for binding of CD28 to CD80 (FIG. 1A) and that CD28, CTLA-4, and PD-L2 did not compete for binding of PD-L1 to CD80 (FIG. 1B). Thus, these results demonstrated that CD28 and PD-L1 are non-competitive binders of CD80, and that this non-competitive binding can be demonstrated independently of which ligand is being detected in the ELISA.

Example 8 Generation and Assessment of Stacked Molecules Containing Different Affinity-Modified Domains

Selected variant molecules described above that were affinity-modified for one or more counter structure ligand were used to generate “stack” molecule (i.e., Type II immunomodulatory protein) containing two or more affinity-modified IgSF domains. Stack constructs were obtained as geneblocks (Integrated DNA Technologies, Coralville, Iowa) that encode the stack in a format that enables its fusion to Fc by standard Gibson assembly using a Gibson assembly kit (New England Biolabs).

The encoding nucleic acid molecule of all stacks was generated to encode a protein designed as follows: Signal peptide, followed by the first variant IgV of interest, followed by a 15 amino acid linker which is composed of three GGGGS(G4S) motifs (SEQ ID NO:228), followed by the second IgV of interest, followed by two GGGGS linkers (SEQ ID NO: 229) followed by three alanines (AAA), followed by a human IgG1 Fc as described above. To maximize the chance for correct folding of the IgV domains in each stack, the first IgV was preceded by all residues that normally occur in the wild-type protein between this IgV and the signal peptide (leading sequence). Similarly, the first IgV was followed by all residues that normally connect it in the wild-type protein to either the next Ig domain (typically an IgC domain) or if such a second IgV domain is absent, the residues that connect it to the transmembrane domain (trailing sequence). The same design principle was applied to the second IgV domain except that when both IgV domains were derived from same parental protein (e.g. a CD80 IgV stacked with another CD80 IgV), the linker between both was not duplicated.

Table 9 sets forth the design for exemplary stacked constructs. The exemplary stack molecules shown in Table 9 contain the IgV domains as indicated and additionally leading or trailing sequences as described above. In the Table, the following components are present in order: signal peptide (SP; SEQ ID NO:225), IgV domain 1 (IgV1), trailing sequence 1 (TS1), linker 1 (LR1; SEQ ID NO:228), IgV domain 2 (IgV2), trailing sequence 2 (TS2), linker 2 (LR2; SEQ ID NO:230) and Fc domain (SEQ ID NO:226 containing C5S/N82G amino acid substitution). In some cases, a leading sequence 1 (LS1) is present between the signal peptide and IgV1 and in some cases a leading sequence 2 (LS2) is present between the linker and IgV2.

TABLE 9 Amino acid sequence (SEQ ID NO) of components of exemplary stacked constructs First domain Second domain SP LS1 IgV1 TS1 LR1 LS2 IgV2 TS2 LR2 Fc NKp30 WT + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + ICOSL WT NO: 214 NO: 235 NO: 196 NO: 233 NKp30 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + L30V/A60V/S64P/ NO: 215 NO: 235 NO: 212 NO: 233 S86G ICOSL N52S/N57Y/H94D/ L96F/L98F/Q100R NKp30 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + L30V/A60V/S64P/ NO: 215 NO: 235 NO: 199 NO: 233 S86G) ICOSL N52D NKp30 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + L30V/A60V/S64P/ NO: 215 NO: 235 NO: 201 NO: 233 S86G ICOSL N52H/N57Y/Q100P ICOSL WT + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + Nkp30 WT NO: 196 NO: 233 NO: 214 NO: 235 ICOSL N52D + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + NKp30 NO: 199 NO: 233 NO: 215 NO: 235 L30V/A60V/S64P/ S86G ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52H/N57Y/Q100P NO: 201 NO: 233 NO: 215 NO: 235 NKp30 L30V/A60V/S64P/ S86G Domain 1: NKp30 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + WT NO: 214 NO: 235 NO: 152 NO: 231 Domain 2: CD80 WT Domain 1: NKp30 + − SEQ ID SEQ ID + SEQ ID SEQ ID SEQ ID + + WT NO: 214 NO: 235 NO: 236 NO: 220 NO: 237 Domain 2: CD86 WT Domain 1: NKp30 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + L30V/A60V/S64P/ NO: 215 NO: 235 NO: 192 NO: 231 S86G Domain 2: CD80 R29H/Y31H/T41G/ Y87N/E88G/K89E/ D90N/A91G/P109S Domain 1: NKp30 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + L30V/A60V/S64P/ NO: 215 NO: 235 NO: 175 NO: 231 S86G Domain 2: CD80 I67T/L70Q/A91G/ T120S Domain 1: NKp30 + − SEQ ID SEQ ID + SEQ ID SEQ ID SEQ ID + + L30V/A60V/S64P/ NO: 215 NO: 235 NO: 236 NO: 221 NO: 237 S86G Domain 2: CD86 Q35H/H90L/Q102H Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + WT NO: 152 NO: 231 NO: 214 NO: 235 Domain 2: Nkp30 WT Domain 1: CD86 + SEQ ID SEQ ID SEQ ID + − SEQ ID SEQ ID + + WT NO: 236 NO: 220 NO: 237 NO: 214 NO: 235 Domain 2: Nkp30 WT Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + R29H/Y31H/T41G/ NO: 192 NO: 231 NO: 215 NO: 235 Y87N/E88G/K89E/ D90N/A91G/P109S Domain 2: NKp30 L30V/A60V/S64P/ S86G Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + I67T/L70Q/A91G/ NO: 175 NO: 231 NO: 215 NO: 235 T120S Domain 2: NKp30 L30V/A60V/S64P/ S86G Domain 1: CD86 + SEQ ID SEQ ID SEQ ID + − SEQ ID SEQ ID + + Q35H/H90L/Q102H NO: 236 NO: 221 NO: 237 NO: 215 NO: 235 Domain 2: NKp30 L30V/A60V/S64P/ S86G Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + WT NO: 152 NO: 231 NO: 196 NO: 233 Domain 2: ICOSL WT Domain 1: CD80 + − SEQ ID SEQ ID + SEQ ID SEQ ID SEQ ID + + WT NO: 152 NO: 231 NO: 236 NO: 220 NO: 237 Domain 2: CD86 WT Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + WT NO: 152 NO: 231 NO: 152 NO: 231 Domain 2: CD80 WT Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + E88D/K89R/D90K/ NO: 189 NO: 231 NO: 192 NO: 231 A91G/F92Y/K93R Domain 2: CD80 R29H/Y31H/T41G/ Y87N/E88G/K89E/ D90N/A91G/P109S Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + A12T/H18L/N43V/ NO: 193 NO: 231 NO: 192 NO: 231 F59L/E77K/P109S/ I118T Domain 2: CD80 R29H/Y31H/T41G/ Y87N/E88G/K89E/ D90N/A91G/P109S Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + A12T/H18L/N43V/ NO: 193 NO: 231 NO: 175 NO: 231 F59L/E77K/P109S/ I118T Domain 2: CD80 I67T/L70Q/A91G/ T120S Domain 1: CD80 + − SEQ ID SEQ ID + SEQ ID SEQ ID SEQ ID + + E88D/K89R/D90K/ NO: 189 NO: 231 NO: 236 NO: 221 NO: 237 A91G/F92Y/K93R Domain 2: CD86 Q35H/H90L/Q102H Domain 1: CD80 + − SEQ ID SEQ ID + SEQ ID SEQ ID SEQ ID + + A12T/H18L/N43V/ NO: 193 NO: 231 NO: 236 NO: 221 NO: 237 F59L/E77K/P109S/ I118T Domain 2: CD86 Q35H/H90L/Q102H Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + E88D/K89R/D90K/ NO: 189 NO: 231 NO: 213 NO: 233 A91G/F92Y/K93R Domain 2: ICOSL N525/N57Y/H94D/ L96F/L98F/Q100R/ G103E/F120S Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + A12T/H18L/N43V/ NO: 193 NO: 231 NO: 213 NO: 233 F59L/E77K/P109S/ I118T Domain 2: ICOSL N52S/N57Y/H94D/ L96F/L98F/Q100R/ G103E/F120S Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + A12T/H18L/N43V/ NO: 193 NO: 231 NO: 199 NO: 233 F59L/E77K/P109S/ I118T Domain 2: ICOSL N52D Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + E88D/K89R/D90K/ NO: 189 NO: 231 NO: 201 NO: 233 A91G/F92Y/K93R Domain 2: ICOSL N52H/N57Y/Q100P Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + A12T/H18L/N43V/ NO: 193 NO: 231 NO: 201 NO: 233 F59L/E77K/P109S/ I118T Domain 2: ICOSL N52H/N57Y/Q100P Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + WT NO: 196 NO: 233 NO: 152 NO: 231 Domain 2: CD80 WT Domain 1: CD86 + SEQ ID SEQ ID SEQ ID + − SEQ ID SEQ ID + + WT NO: 236 NO: 220 NO: 237 NO: 152 NO: 231 Domain 2: CD80 WT Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + R29H/Y31H/T41G/ NO: 192 NO: 231 NO: 189 NO: 231 Y87N/E88G/K89E/ D90N/A91G/P109S Domain 2: CD80 E88D/K89R/D90K/ A91G/F92Y/K93R Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + R29H/Y31H/T41G/ NO: 192 NO: 231 NO: 193 NO: 231 Y87N/E88G/K89E/ D90N/A91G/P109S Domain 2: CD80 A12T/H18L/N43V/ F59L/E77K/P109S/ I118T Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + I67T/L70Q/A91G/ NO: 175 NO: 231 NO: 189 NO: 231 T120S Domain 2: CD80 E88D/K89R/D90K/ A91G/F92Y/K93R Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + I67T/L70Q/A91G/ NO: 175 NO: 231 NO: 193 NO: 231 T120S Domain 2: CD80 A12T/H18L/N43V/ F59L/E77K/P109S/ I118T Domain 1: CD86 + SEQ ID SEQ ID SEQ ID + − SEQ ID SEQ ID + + Q35H/H90L/Q102H NO: 236 NO: 221 NO: 237 NO: 189 NO: 231 Domain 2: CD80 E88D/K89R/D90K/ A91G/F92Y/K93R Domain 1: CD86 + SEQ ID SEQ ID SEQ ID + − SEQ ID SEQ ID + + Q35H/H90L/Q102H NO: 236 NO: 221 NO: 237 NO: 193 NO: 231 Domain 2: CD80 A12T/H18L/N43V/ F59L/E77K/P109S/ I118T Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N525/N57Y/H94D/ NO: 213 NO: 233 NO: 189 NO: 231 L96F/L98F/Q100R/ G103E/F120S Domain 2: CD80 E88D/K89R/D90K/ A91G/F92Y/K93R Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52S/N57Y/H94D/ NO: 213 NO: 233 NO: 193 NO: 231 L96F/L98F/Q100R/ G103E/F120S Domain 2: CD80 A12T/H18L/N43V/ F59L/E77K/P109S/ I118T Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52D NO: 199 NO: 233 NO: 189 NO: 231 Domain 2: CD80 E88D/K89R/D90K/ A91G/F92Y/K93R Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52D NO: 199 NO: 233 NO: 193 NO: 231 Domain 2: CD80 A12T/H18L/N43V/ F59L/E77K/P109S/ I118T Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52H/N57Y/Q100P NO: 201 NO: 233 NO: 189 NO: 231 Domain 2: CD80 E88D/K89R/D90K/ A91G/F92Y/K93R Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52H/N57Y/Q100P NO: 201 NO: 233 NO: 193 NO: 231 Domain 2: CD80 A12T/H18L/N43V/ F59L/E77K/P109S/ I118T Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + V68M/L70P/L72P/ NO: 195 NO: 231 NO: 189 NO: 231 K86E Domain 2: CD80 E88D/K89R/D90K/ A91G/F92Y/K93R Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + R29V/Y31F/K36G/ NO: 194 NO: 231 NO: 189 NO: 231 M38L/N43Q/E81R/ V83I/L85I/K89R/ D90L/A91E/F92N/ K93Q/R94G Domain 2: CD80 E88D/K89R/D90K/ A91G/F92Y/K93R Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + V68M/L70P/L72P/ NO: 195 NO: 231 NO: 193 NO: 231 K86E Domain 2: CD80 A12T/H18L/N43V/ F59L/E77K/P109S/ I118T Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + R29V/Y31F/K36G/ NO: 194 NO: 231 NO: 193 NO: 231 M38L/N43Q/E81R/ V83I/L85I/K89R/ D90L/A91E/F92N/ K93Q/R94G Domain 2: CD80 A12T/H18L/N43V/ F59L/E77K/P109S/ I118T Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + E88D/K89R/D90K/ NO: 189 NO: 231 NO: 195 NO: 231 A91G/F92Y/K93R Domain 2: CD80 V68M/L70P/L72P/ K86E Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + E88D/K89R/D90K/ NO: 189 NO: 231 NO: 194 NO: 231 A91G/F92Y/K93R Domain 2: CD80 R29V/Y31F/K36G/ M38L/N43Q/E81R/ V83I/L85I/K89R/ D90L/A91E/F92N/ K93Q/R94G Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + A12T/H18L/N43V/ NO: 193 NO: 231 NO: 195 NO: 231 F59L/E77K/P109S/ I118T Domain 2: CD80 V68M/L70P/L72P/ K86E Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + A12T/H18L/N43V/ NO: 193 NO: 231 NO: 194 NO: 231 F59L/E77K/P109S/ I118T Domain 2: CD80 R29V/Y31F/K36G/ M38L/N43Q/E81R/ V83I/L851/K89R/ D90L/A91E/F92N/ K93Q/R94G Domain 1: CD86 + SEQ ID SEQ ID SEQ ID + − SEQ ID SEQ ID + + WT NO: 236 NO: 220 NO: 237 NO: 196 NO: 233 Domain 2: ICOSL WT Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + R29H/Y31H/T41G/ NO: 192 NO: 231 NO: 213 NO: 233 Y87N/E88G/K89E/ D90N/A91G/P109S Domain 2: ICOSL N52S/N57Y/H94D/ L96F/L98F/Q100R/ G103E/F120S Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + I67T/L70Q/A91G/ NO: 175 NO: 231 NO: 213 NO: 233 T120S Domain 2: ICOSL N52S/N57Y/H94D/ L96F/L98F/Q100R/ G103E/F120S Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + R29H/Y31H/T41G/ NO: 192 NO: 231 NO: 199 NO: 233 Y87N/E88G/K89E/ D90N/A91G/P109S Domain 2: ICOSL N52D Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + I67T/L70Q/A91G/ NO: 175 NO: 231 NO: 199 NO: 233 T120S Domain 2: ICOSL N52D Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + R29H/Y31H/T41G/ NO: 192 NO: 231 NO: 201 NO: 233 Y87N/E88G/K89E/ D90N/A91G/P109S Domain 2: ICOSL N52H/N57Y/Q100P Domain 1: CD80 + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + I67T/L70Q/A91G/ NO: 175 NO: 231 NO: 201 NO: 233 T120S Domain 2: ICOSL N52H/N57Y/Q100P Domain 1: CD86 + SEQ ID SEQ ID SEQ ID + − SEQ ID SEQ ID + + Q35H/H90L/Q102H NO: 236 NO: 221 NO: 237 NO: 213 NO: 233 Domain 2: ICOSL N52S/N57Y/H94D/ L96F/L98F/Q100R/ G103EF120S Domain 1: CD86 + SEQ ID SEQ ID SEQ ID + − SEQ ID SEQ ID + + Q35H/H90L/Q102H NO: 236 NO: 221 NO: 237 NO: 199 NO: 233 Domain 2: ICOSL N52D Domain 1: CD86 + SEQ ID SEQ ID SEQ ID + − SEQ ID SEQ ID + + Q35H/H90L/Q102H NO: 236 NO: 221 NO: 237 NO: 201 NO: 233 Domain 2: ICOSL N52H/N57Y/Q100P Domain 1: ICOSL + − SEQ ID SEQ ID + SEQ ID SEQ ID SEQ ID + + WT NO: 196 NO: 233 NO: 236 NO: 220 NO: 237 Domain 2: CD86 WT Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52S/N57Y/H94D/ NO: 213 NO: 233 NO: 192 NO: 231 L96F/L98F/Q100R/ G103E/F120S Domain 2: CD80 R29H/Y31H/T41G/ Y87N/E88G/K89E/ D90N/A91G/P109S Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52S/N57Y/H94D/ NO: 213 NO: 233 NO: 175 NO: 231 L96F/L98F/Q100R/ G103E/F120S Domain 2: CD80 I67T/L70Q/A91G/ T120S Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52D NO: 199 NO: 233 NO: 192 NO: 231 Domain 2: CD80 R29H/Y31H/T41G/ Y87N/E88G/K89E/ D90N/A91G/P109S Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52D NO: 199 NO: 233 NO: 175 NO: 231 Domain 2: CD80 I67T/L70Q/A91G/ T120S Domain 1: ICOSL + − SEQ ID SEQ ID + − SEQ ID SEQ ID + + N52H/N57Y/Q100P NO: 201 NO: 233 NO: 192 NO: 231 Domain 2: CD80 R29H/Y31H/T41G/ Y87N/E88G/K89E/ D90N/A91G/P109S Domain 1: ICOSL + − SEQ ID SEQ ID + SEQ ID SEQ ID SEQ ID + + N52S/N57Y/H94D/ NO: 213 NO: 233 NO: 236 NO: 221 NO: 237 L96F/L98F/Q100R/ G103E/F120S Domain 2: CD86 Q35H/H90L/Q102H Domain 1: ICOSL + − SEQ ID SEQ ID + SEQ ID SEQ ID SEQ ID + + N52D NO: 199 NO: 233 NO: 236 NO: 221 NO: 237 Domain 2: CD86 Q35H/H90L/Q102H Domain 1: ICOSL + − SEQ ID SEQ ID + SEQ ID SEQ ID SEQ ID + + N52H/N57Y/Q100P NO: 201 NO: 233 NO: 236 NO: 221 NO: 237 Domain 2: CD86 Q35H/H90L/Q102H

High throughput expression and purification of the variant IgV-stacked-Fc fusion molecules containing various combinations of variant IgV domains from CD80, CD86, ICOSL or Nkp30 containing at least one affinity-modified IgV domain were generated as described in Example 5. Binding of the variant IgV-stacked-Fc fusion molecules to respective counter structures and functional activity by anti-CD3 coimmobilization assay also were assessed as described in Example 6. For example, costimulatory bioactivity of the stacked IgSF Fc fusion proteins was determined in a similar immobilized anti-CD3 assay as above. In this case, 4 nM of anti-CD3 (OKT3, Biolegend, USA) was coimmobilized with 4 nM to 120 nM of human rB7-H6.Fc (R&D Systems, USA) or human rPD-L1.Fc (R&D Systems, USA) overnight on tissue-culture treated 96 well plates (Corning, USA). The following day unbound protein was washed off with PBS and 100,000 purified pan T cells were added to each well in 100 ul Ex-Vivo 15 media (Lonza, Switzerland). The stacked IgSF domains were subsequently added at concentrations ranging from 8 nM to 40 nM in a volume of 100 ul for 200 ul volume total. Cells were cultured 3 days before harvesting culture supernatants and measuring human IFN-gamma levels with Duoset ELISA kit (R&D Systems, USA) as mentioned above.

The results are set forth in Tables 10-14. Specifically, Table 10 sets forth binding and functional activity results for variant IgV-stacked-Fc fusion molecules containing an NKp30 IgV domain and an ICOSL IgV domain. Table 11 sets forth binding and functional activity results for variant IgV-stacked-Fv fusion molecules containing an Nkp30 IgV domain and a CD80 or CD86 IgV domain. Table 12 sets forth binding and functional activity results for variant IgV-stacked-Fc fusion molecules containing a variant CD80 IgV domain and a CD80, CD86 or ICOSL IgV domain. Table 13 sets forth binding and functional activity results for variant IgV-stacked-Fc fusion molecules containing two variant CD80 IgV domains. Table 14 sets forth results for variant IgV-stacked Fc fusion molecules containing a variant CD80 or CD86 IgV domain and a variant ICOSL IgV domain.

For each of Tables 10-14, Column 1 indicates the structural organization and orientation of the stacked, affinity modified or wild-type (WT) domains beginning with the amino terminal (N terminal) domain, followed by the middle WT or affinity modified domain located before the C terminal human IgG1 Fc domains. Column 2 sets forth the SEQ ID NO identifier for the sequence of each IgV domain contained in a respective “stack” molecule. Column 3 shows the binding partners which the indicated affinity modified stacked domains from column 1 were selected against.

Also shown is the binding activity as measured by the Mean Fluorescence Intensity (MFI) value for binding of each stack molecule to cells engineered to express various counter structure ligands and the ratio of the MFI compared to the binding of the corresponding stack molecule containing unmodified IgV domains not containing the amino acid substitution(s) to the same cell-expressed counter structure ligand. The functional activity of the variant stack molecules to modulate the activity of T cells also is shown based on the calculated levels of IFN-gamma in culture supernatants (pg/ml) generated with the indicated variant stack molecule in solution and the appropriate ligand coimmoblized with anti-CD3 as described in Example 6. The Tables also depict the ratio of IFN-gamma produced by each variant stack molecule compared to the corresponding unmodified stack molecule in the coimmobilization assay.

As shown, the results showed that it was possible to generate stack molecules containing at least one variant IgSF domains that exhibited affinity-modified activity of increased binding for at least one cognate counter structure ligand compared to a corresponding stack molecule containing the respective unmodified (e.g. wild-type) IgV domain. In some cases, the stack molecule, either from one or a combination of both variant IgSF domains in the molecule, exhibited increased binding for more than one cognate counter structure ligand. The results also showed that the order of the IgV domains in the stacked molecules could, in some cases, alter the degree of improved binding activity. In some cases, functional T cell activity also was altered when assessed in the targeted coimmobilization assay.

TABLE 10 Stacked variant IgV Fc fusion proteins containing an NKp30 IgV domain and an ICOS IgV domain Anti-CD3 Binding Activity coimmobilization Counter B7H6 MFI ICOS MFI CD28 MFI assay pg/ml Domain Structure SEQ ID structure (WT (WT (WT IFN-gamma N terminal to C terminal: NO selected parental parental parental (WT parental domain 1/domain 2/Fc (IgV) against MFI ratio) MFI ratio) MFI ratio) IFN-gamma ratio) Domain 1: NKp30 WT 214 — 64538 26235 6337 235 Domain 2: ICOSL WT 196 (1.00) (1.00) (1.00) (1.00) Domain 1: NKp30 (L30V 215 B7-H6 59684 12762 9775 214 A60V S64P S86G) (0.92) (0.49) (1.54) (0.91) Domain 2: ICOSL (N52S 212 ICOS- N57Y H94D L96F L98F CD28 Q100R) Domain 1: NKp30 (L30V 215 B7-H6 65470 30272 9505 219 A60V S64P S86G) (1.01) (1.15) (1.50) (0.93) Domain 2: ICOSL (N52D) 199 ICOS- CD28 Domain 1: NKp30 (L30V 215 B7-H6 38153 27903 11300 189 A60V S64P S86G)/ (0.59) (1.06) (1.78) (0.80) Domain 2: ICOSL (N52H 201 ICOS- N57Y Q100P) CD28 Domain 1: ICOSL WT 196 — 117853 70320 7916 231 Domain 2: Nkp30 WT 214 (1.0) (1.0) (1.0) (1.0) Domain 1: ICOSL (N52D) 199 ICOS- 100396 83912 20778 228 CD28 (0.85) (1.19) (2.62) (0.98) Domain 2: NKp30 (L30V 215 B7-H6 A60V S64P S86G) Domain 1: ICOSL (N52H 201 ICOS- 82792 68874 72269 561 N57Y Q100P) CD28 (0.70) (0.98) (9.12) (2.43) Domain 2: NKp30 (L30V 215 B7-H6 A60V S64P S86G)

TABLE 11 Stacked variant IgV Fc fusion proteins containing an NKp30 IgV domain and a CD80 or CD86 IgV domain Anti-CD3 coimmobilization Counter Binding Activity assay Domain Structure SEQ structure B7H6 MFI CD28 MFI pg/ml IFN-gamma N terminal to C terminal: ID NO selected (WT parental (WT parental (WT parental IFN- domain 1/domain 2/Fc (IgV) against MFI ratio) MFI ratio) gamma ratio) Domain 1: NKp30 WT 214 — 88823 7022 68 Domain 2: CD80 WT 152 (1.00) (1.00) (1.00) Domain 1: NKp30 WT 214 — 14052 1690 92 Domain 2: CD86 WT 220 (1.00) (1.00) (1.00) Domain 1: NKp30 (L30V 215 B7-H6 53279 9027 94 A60V S64P S86G) (0.60) (1.29) (1.38) Domain 2: CD80 192 CD28 R29H/Y31H/T41G/Y87N/ E88G/K89E/D90N/A91G/ P109S Domain 1: NKp30 (L30V 215 B7-H6 41370 11240 60 A60V S64P S86G) (0.47) (1.60) (0.88) Domain 2: CD80 175 CD28 167T/L70Q/A91G/T120S Domain 1: NKp30 (L30V 215 B7-H6 68480 9115 110 A60V S64P S86G)/ (4.87) (5.39) (1.19) Domain 2: CD86 221 CD28 Q35H/H90L/Q102H Domain 1: CD80 WT 152 — 110461 13654 288 Domain 2: Nkp30 WT 214 (1.00) (1.00) (1.00) Domain 1: CD86 WT 220 CD28 128899 26467 213 Domain 2: Nkp30 WT 214 B7-H6 (1.00) (1.00) (1.00) Domain 1: CD80 192 CD28 55727 4342 100 R29H/Y31H/T41G/Y87N/ (0.50) (0.32) (0.35) E88G/K89E/D90N/A91G/ P109S Domain 2: NKp30 (L30V 215 B7-H6 A60V S64P S86G) Domain 1: CD80 175 CD28 40412 7094 84 167T/L70Q/A91G/T120S (0.37) (0.52) (0.29) Domain 2: NKp30 (L30V 215 B7-H6 A60V S64P S86G) Domain 1: CD86 221 CD28 220836 11590 113 Q35H/H90L/Q102H (1.71) (0.44) (0.53) Domain 2: NKp30 (L30V 215 B7-H6 A60V S64P S86G)

TABLE 12 Stacked variant IgV Fc fusion proteins containing a CD80 IgV domain and a CD80, CD86, or ICOSL IgV domain Anti-CD3 Binding Activity coimmobilization SEQ Counter CD28 MFI PD-L1 ICOS assay pg/ml Domain Structure ID structure (WT MFI (WT MFI (WT IFN-gamma N terminal to C terminal: NO selected parental parental parental (WT parental domain 1/domain 2/Fc (IgV) against MFI ratio) MFI ratio) MFI ratio) IFN-gamma ratio) Domain 1: CD80 WT 152 1230 2657 11122 69 Domain 2: ICOSL WT 196 (1.00) (1.00) (1.00) (1.00) Domain 1: CD80 WT 152 60278 2085 59 Domain 2: CD86 WT 220 (1.00) (1.00) (1.00) Domain 1: CD80 WT 152 1634 6297 98 Domain 2: CD80 WT 152 (1.00) (1.00) (1.00) Domain 1: CD80 189 PD-L1 4308 4234 214 E88D/K89R/D90K/A91G/ (2.64) (0.67) (2.18) F92Y/K93R Domain 2: CD80 192 CD28 R29H/Y31H/T41G/Y87N/ E88G/K89E/D90N/A91G/ P109S Domain 1: CD80 193 PD-L1 7613 2030 137 A12T/H18L/N43V/F59L/ (4.66) (0.32) (1.40) E77K/P109S/I118T Domain 2: CD80 192 CD28 R29H/Y31H/T41G/Y87N/ E88G/K89E/D90N/A91G/ P109S Domain 1: CD80 193 PD-L1 3851 3657 81 A12T/H18L/N43V/F59L/ (2.36) (0.58) (0.83) E77K/P109S/I118T Domain 2: CD80 175 CD28 I67T/L70Q/A91G/T120S Domain 1: CD80 189 PD-L1 4117 2914 96 E88D/K89R/D90K/A91G/ (0.07) (1.40) (1.63) F92Y/K93R Domain 2: CD86 221 CD28 Q35H/H90L/Q102H Domain 1: CD80 193 PD-L1 2868 3611 94 A12T/H18L/N43V/F59L/ (0.05) (1.73) (1.60) E77K/P109S/I118T Domain 2: CD86 221 CD28 Q35H/H90L/Q102H Domain 1: CD80 189 PD-L1 3383 4515 5158 90 E88D/K89R/D90K/A91G/ (2.75) (1.70) (0.46) (1.30) F92Y/K93R Domain 2: ICOSL 213 ICOS/ N52S/N57Y/H94D/L96F/ CD28 L98F/Q100R/G103E/ F120S Domain 1: CD80 193 PD-L1 2230 2148 3860 112 A12T/H18L/N43V/F59L/ (1.81) (0.81) (0.35) (1.62) E77K/P109S/I118T Domain 2: ICOSL 213 ICOS/ N52S/N57Y/H94D/L96F/ CD28 L98F/Q100R/G103E/ F120S Domain 1: CD80 193 PD-L1 5665 6446 15730 126 A12T/H18L/N43V/F59L/ ICOS/ (4.61) (2.43) (1.41) (1.83) E77K/P109S/I118T CD28 Domain 2: ICOSL 199 N52D Domain 1: CD80 189 PD-L1 6260 4543 11995 269 E88D/K89R/D90K/A91G/ (5.09) (1.71) (1.08) (3.90) F92Y/K93R Domain 2: ICOSL 201 ICOS/ N52H/N57Y/Q100P CD28 Domain 1: CD80 193 PD-L1 3359 3874 8541 97 A12T/H18L/N43V/F59L/ (2.73) (1.46) (0.77) (1.41) E77K/P109S/I118T Domain 2: ICOSL 201 ICOS/ N52H/N57Y/Q100P CD28 Domain 1: ICOSL WT 196 3000 2966 14366 101 Domain 2: CD80 WT 152 (1.00) (1.00) (1.00) (1.00) Domain 1: CD86 WT 220 4946 1517 125 Domain 2: CD80 WT 152 (1.00) (1.00) (1.00) Domain 1: CD80 192 CD28 2832 3672 114 R29H/Y31H/T41G/Y87N/ (1.73) (0.58) (1.16) E88G/K89E/D90N/A91G/ P109S Domain 2: CD80 189 PD-L1 E88D/K89R/D90K/A91G/ F92Y/K93R Domain 1: CD80 192 CD28 4542 2878 142 R29H/Y31H/T41G/Y87N/ (2.78) (0.45) (1.45) E88G/K89E/D90N/A91G/ P109S Domain 2: CD80 193 PD-L1 A12T/H18L/N43V/F59L/ E77K/P109S/I118T Domain 1: CD80 175 CD28 938 995 102 I67T/L70Q/A91G/T120S (0.57) (0.16) (1.04) Domain 2: CD80 189 PD-L1 E88D/K89R/D90K/A91G/ F92Y/K93R Domain 1: CD80 175 CD28 4153 2827 108 I67T/L70Q/A91G/T120S Domain 2: CD80 193 PD-L1 (2.54) (0.45) (1.10) A12T/H18L/N43V/F59L/ E77K/P109S/I118T Domain 1: CD86 221 CD28 14608 2535 257 Q35H/H90L/Q102H (2.95) (1.67) (2.06) Domain 2: CD80 189 PD-L1 E88D/K89R/D90K/A91G/ F92Y/K93R Domain 1: CD86 221 CD28 2088 2110 101 Q35H/H90L/Q102H (0.42) (1.39) (0.81) Domain 2: CD80 193 PD-L1 A12T/H18L/N43V/F59L/ E77K/P109S/I118T Domain 1: ICOSL 213 ICOS/ 3634 4893 6403 123 N52S/N57Y/H94D/L96F/ CD28 (1.21) (1.65) (0.45) (1.22) L98F/Q100R/G103E/ F120S Domain 2: CD80 189 PD-L1 E88D/K89R/D90K/A91G/ F92Y/K93R Domain 1: ICOSL 213 ICOS/ 1095 5929 7923 127 N52S/N57Y/H94D/L96F/ CD28 (0.37) (2.0) (0.55) (1.26) L98F/Q100R/G103E/ F120S Domain 2: CD80 193 PD-L1 A12T/H18L/N43V/F59L/ E77K/P109S/I118T Domain 1: ICOSL 199 ICOSL/ 2023 5093 16987 125 N52D CD28 (0.67) (1.72) (1.18) (1.24) Domain 2: CD80 189 PD-L1 E88D/K89R/D90K/A91G/ F92Y/K93R Domain 1: ICOSL 199 ICOS/ 3441 3414 20889 165 N52D CD28 (1.15) (1.15) (1.45) (1.63) Domain 2: CD80 193 PD-L1 A12T/H18L/N43V/F59L/ E77K/P109S/I118T Domain 1: ICOSL 201 ICOS/ 7835 6634 20779 95 N52H/N57Y/Q100P CD28 (2.61) (2.24) (1.45) (0.94) Domain 2: CD80 189 PD-L1 E88D/K89R/D90K/A91G/ F92Y/K93R Domain 1: ICOSL 201 ICOS/ 8472 3789 13974 106 N52H/N57Y/Q100P CD28 (2.82) (1.28) (0.97) (1.05) Domain 2: CD80 193 PD-L1 A12T/H18L/N43V/F59L/ E77K/P1098/I118T

TABLE 13 Stacked variant IgV Fc fusion proteins containing two CD80 IgV domains Counter Binding Activity Functional Domain Structure SEQ ID structure PD-L1 MFI CTLA-4 MFI Activity MLR N terminal to C terminal: NO selected (WT parental (WT parental IFN-gamma domain 1/domain 2/Fc (IgV) against MFI ratio) MFI ratio) pg/ml Domain 1: CD80 WT 152 6297 4698 35166 Domain 2: CD80 WT 152 (1.00) (1.00) (1.00) Domain 1: CD80 195 CTLA-4 2464 4955 5705 V68M/L70P/L72P/K86E (0.39) (1.05) (0.16) Domain 2: CD80 189 PD-L1 E88D/K89R/D90K/A91G/ F92Y/K93R Domain 1: CD80 194 CTLA-4 1928 1992 1560 R29V/Y31F/K36G/M38L/N43Q/ (0.31) (0.42) (0.04) E81R/V83I/L85I/K89R/D90L/ A91E/F92N/K93Q/R94G Domain 2: CD80 189 PD-L1 E88D/K89R/D90K/A91G/ F92Y/K93R Domain 1: CD80 195 CTLA-4 1215 1382 2171 V68M/L70P/L72P/K86E (0.19) (0.29) (0.06) Domain 2: CD80 193 PD-L1 A12T/H18L/N43V/F59L/ E77K/P109S/I118T Domain 1: CD80 194 CTLA-4 1592 1962 1512 R29V/Y31F/K36G/M38L/N43Q/ (0.25) (0.42) (0.04) E81R/V83I/L85I/K89R/D90L/ A91E/F92N/K93Q/R94G Domain 2: CD80 193 PD-L1 A12T/H18L/N43V/F59L/E77K/ P109S/I118T Domain 1: CD80 189 PD-L1 1747 2057 9739 E88D/K89R/D90K/A91G/ (0.28) (0.44) (0.28) F92Y/K93R Domain 2: CD80 195 CTLA-4 V68M/L70P/L72P/K86E Domain 1: CD80 189 PD-L1 1752 1772 5412 E88D/K89R/D90K/A91G/ (0.28) (0.38) (0.15) F92Y/K93R Domain 2: CD80 194 CTLA-4 R29V/Y31F/K36G/M38L/N43Q/ E81R/V83I/L85I/K89R/D90L/ A91E/F92N/K93Q/R94G Domain 1: CD80 193 PD-L1 1636 1887 7608 A12T/H18L/N43V/F59L/E77K/ (0.26) (0.40) (0.22) P109S/I118T Domain 2: CD80 195 CTLA-4 V68M/L70P/L72P/K86E Domain 1: CD80 193 PD-L1 2037 4822 11158 A12T/H18L/N43V/F59L/E77K/ (0.32) (1.03) (0.32) P109S/I118T Domain 2: CD80 194 CTLA-4 R29V/Y31F/K36G/M38L/N43Q/ E81R/V83I/L85I/K89R/D90L/ A91E/F92N/K93Q/R94G

TABLE 14 Stacked variant IgV Fc fusion proteins containing a CD80 or CD86 IgV domain and an ICOSL IgV domain Counter Binding Activity Functional Domain Structure SEQ ID structure PD-L1 MFI CTLA-4 MFI Activity MLR N terminal to C terminal: NO selected (WT parental (WT parental IFN-gamma domain 1/domain 2/Fc (IgV) against MFI ratio) MFI ratio) pg/ml Domain 1: CD80 WT 152 1230 11122 1756 Domain 2: ICOSL WT 196 (1.00) (1.00) (1.00) Domain 1: CD86 WT 220 29343 55193 6305 Domain 2: ICOSL WT 196 (1.00) (1.00) (1.00) Domain 1: CD80 192 CD28 2280 3181 2281 R29H/Y31H/T41G/Y87N/E88G/ (1.85) (0.29) (1.30) K89E/D90N/A91G/P109S Domain 2: ICOSL 213 ICOS/CD28 N52S/N57Y/H94D/L96F/L98F/ Q100R/G103E/F120S Domain 1: CD80 175 CD28 2309 26982 1561 I67T/L70Q/A91G/T120S (1.88) (2.43) (0.89) Domain 2: ICOSL 213 ICOS/CD28 N52S/N57Y/H94D/L96F/L98F/ Q100R/G103E/F120S Domain 1: CD80 192 CD28 4285 22744 1612 R29H/Y31H/T41G/Y87N/E88G/ (3.48) (2.04) (0.92) K89E/D90N/A91G/P109S Domain 2: ICOSL 199 ICOS/CD28 N52D Domain 1: CD80 175 CD28 3024 16916 3857 I67T/L70Q/A91G/T120S (2.46) (1.52) (2.20) Domain 2: ICOSL 199 ICOS/CD28 N52D Domain 1: CD80 192 CD28 6503 7240 6886 R29H/Y31H/T41G/Y87N/E88G/ (5.29) (0.65) (3.92) K89E/D90N/A91G/P109S Domain 2: ICOSL 201 ICOS/CD28 N52H/N57Y/Q100P Domain 1: CD80 175 CD28 3110 4848 3393 I67T/L70Q/A91G/T120S (2.53) (0.44) (1.93) Domain 2: ICOSL 201 ICOS/CD28 N52H/N57Y/Q100P Domain 1: CD86 221 CD28 Q35H/H90L/Q102H Domain 2: ICOSL 213 ICOS/CD28 11662 21165 880 N52S/N57Y/H94D/L96F/L98F/ (0.40) (0.38) (0.14) Q100R/G103E/F120S Domain 1: CD86 221 CD28 24230 73287 1110 Q35H/H90L/Q102H (0.83) (1.33) (0.18) Domain 2: ICOSL 199 ICOS/CD28 N52D Domain 1: CD86 221 CD28 1962 1630 587 Q35H/H90L/Q102H ICOS/CD28 (0.07) (0.03) (0.09) Domain 2: ICOSL 201 N52H/N57Y/Q100P Domain 1: ICOSL WT 196 3000 14366 4113 Domain 2: CD80 WT 152 (1.00) (1.00) (1.00) Domain 1: ICOSL WT 196 18005 53602 18393 Domain 2: CD86 WT 220 (1.00) (1.00) (1.00) Domain 1: ICOSL 213 ICOSL/CD28 10426 51286 18680 N52S/N57Y/H94D/L96F/L98F/ (3.48) (3.57) (4.54) Q100R/G103E/F120S Domain 2: CD80 192 CD28 R29H/Y31H/T41G/Y87N/E88G/ K89E/D90N/A91G/P109S Domain 1: ICOSL 213 ICOS/CD28 17751 29790 10637 N52S/N57Y/H94D/L96F/L98F/ (5.92) (2.07) (2.59) Q100R/G103E/F120S Domain 2: CD80 175 CD28 I67T/L70Q/A91G/T120S Domain 1: ICOSL 199 ICOS/CD28 2788 25870 6205 N52D (0.93) (1.80) (1.51) Domain 2: CD80 192 CD28 R29H/Y31H/T41G/Y87N/E88G/ K89E/D90N/A91G/P109S Domain 1: ICOSL 199 ICOS/CD28 2522 13569 5447 N52D (0.84) (0.94) (1.32) Domain 2: CD80 175 CD28 I67T/L70Q/A91G/T120S Domain 1: ICOSL 201 ICOS/CD28 N52H/N57Y/Q100P Domain 2: CD80 192 CD28 9701 9187 5690 R29H/Y31H/T41G/Y87N/E88G/ (3.23) (0.64) (1.38) K89E/D90N/A91G/P109S Domain 1: ICOSL 213 ICOS/CD28 27050 21257 8131 N52S/N57Y/H94D/L96F/L98F/ (1.50) (0.40) (0.44) Q100R/G103E/F120S Domain 2: CD86 221 CD28 Q35H/H90L/Q102H Domain 1: ICOSL 199 ICOS/CD28 34803 80210 6747 N52D (1.93) (1.50) (0.37) Domain 2: CD86 221 CD28 Q35H/H90L/Q102H Domain 1: ICOSL 201 ICOS/CD28 5948 4268 26219 N52H/N57Y/Q100P (0.33) (0.08) (1.43) Domain 2: CD86 221 CD28 Q35H/H90L/Q102H

While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby. 

What is claimed is:
 1. An immunomodulatory protein, comprising at least one non-immunoglobulin affinity modified immunoglobulin superfamily (IgSF) domain comprising one or more amino acid substitution(s) in a wild-type IgSF domain, wherein: the at least one affinity modified IgSF domain has increased binding to at least two cognate binding partners compared to the wild-type IgSF domain; and the at least one affinity modified IgSF domain specifically binds non-competitively to the at least two cognate binding partners.
 2. The immunomodulatory protein of claim 1, wherein the at least two cognate binding partners are cell surface molecular species expressed on the surface of a mammalian cell.
 3. The immunomodulatory protein of claim 2, wherein the cell surface molecular species are expressed in cis configuration or trans configuration.
 4. The immunomodulatory protein of claim 2 or claim 3, wherein the mammalian cell is one of two mammalian cells forming an immunological synapse (IS) and each of the cell surface molecular species is expressed on at least one of the two mammalian cells forming the IS.
 5. The immunomodulatory protein of any of claims 2-4, wherein at least one of the mammalian cells is a lymphocyte.
 6. The immunomodulatory protein of claim 5, wherein the lymphocyte is an NK cell or a T cell.
 7. The immunomodulatory protein of any of claims 5-6, wherein binding of the affinity modified IgSF domain modulates immunological activity of the lymphocyte.
 8. The immunomodulatory protein of claim 7, wherein the immunomodulatory protein is capable of effecting increased immunological activity compared the wild-type protein comprising the wild-type IgSF domain.
 9. The immunomodulatory protein of claim 7, wherein the immunomodulatory protein is capable of effecting decreased immunological activity compared to the wild-type protein comprising the wild-type IgSF domain.
 10. The immunomodulatory protein of any of claims 2-9, wherein at least one of the mammalian cells is a tumor cell.
 11. The immunomodulatory protein of any of claims 2-10, wherein the mammalian cells are human cells.
 12. The immunomodulatory protein of any of claims 4-11, wherein the affinity modified IgSF domain is capable of specifically binding to the two mammalian cells forming the IS.
 13. The immunomodulatory protein of any of claims 1-12, wherein the wild-type IgSF domain is from an IgSF family member of a family selected from Signal-Regulatory Protein (SIRP) Family, Triggering Receptor Expressed On Myeloid Cells Like (TREML) Family, Carcinoembryonic Antigen-related Cell Adhesion Molecule (CEACAM) Family, Sialic Acid Binding Ig-Like Lectin (SIGLEC) Family, Butyrophilin Family, B7 family, CD28 family, V-set and Immunoglobulin Domain Containing (VSIG) family, V-set transmembrane Domain (VSTM) family, Major Histocompatibility Complex (MHC) family, Signaling lymphocytic activation molecule (SLAM) family, Leukocyte immunoglobulin-like receptor (LIR), Nectin (Nec) family, Nectin-like (NECL) family, Poliovirus receptor related (PVR) family, Natural cytotoxicity triggering receptor (NCR) family, T cell immunoglobulin and mucin (TIM) family or Killer-cell immunoglobulin-like receptors (KIR) family.
 14. The immunomodulatory protein of any of claims 1-13, wherein the wild-type IgSF domain is from an IgSF member selected from CD80, CD86, PD-L1, PD-L2, ICOS Ligand, B7-H3, B7-H4, CD28, CTLA4, PD-1, ICOS, BTLA, CD4, CD8-alpha, CD8-beta, LAG3, TIM-3, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, CD200R or Nkp30.
 15. The immunomodulatory protein of any of claims 1-14, wherein the wild-type IgSF domain is a human IgSF member.
 16. The immunomodulatory protein of any of claims 1-15, wherein the wild-type IgSF domain is an IgV domain, an IgC1 domain, an IgC2 domain or a specific binding fragment thereof.
 17. The immunomodulatory protein of any of claims 1-16, wherein the affinity-modified IgSF domain is an affinity modified IgV domain, affinity modified IgC1 domain or an affinity modified IgC2 domain or is a specific binding fragment thereof comprising the one or more amino acid substitutions.
 18. The immunomodulatory protein of any of claims 1-17, wherein the immunomodulatory protein comprises at least two non-immunoglobulin affinity modified IgSF domains.
 19. The immunomodulatory protein of claim 18, wherein the at least two non-immunoglobulin affinity modified IgSF domains each comprise one or more different amino acid substitutions in the same wild-type IgSF domain.
 20. The immunomodulatory protein of claim 19, wherein the at least two non-immunoglobulin affinity modified IgSF domains each comprise one or more amino acid substitutions in different wild-type IgSF domains.
 21. The immunomodulatory protein of claim 20, wherein the different wild-type IgSF domains are from different IgSF family members.
 22. The immunomodulatory protein of any of claims 1-17, wherein the immunomodulatory protein comprises only one non-immunoglobulin affinity modified IgSF domain.
 23. The immunomodulatory protein of any of claims 1-22, wherein the affinity-modified IgSF comprises at least 85% sequence identity to a wild-type IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27.
 24. The immunomodulatory protein of claim 23, further comprising a second affinity-modified IgSF, wherein the second affinity-modified IgSF domain comprises at least 85% sequence identity to a wild-type IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27.
 25. The immunomodulatory protein of any of claims 1-24, wherein the wild-type IgSF domain is a member of the B7 family.
 26. The immunomodulatory protein of any of claims 1-25, wherein the wild-type IgSF domain is a domain of CD80, CD86 or ICOSLG.
 27. The immunomodulatory protein of any of claims 1-26, wherein the wild-type IgSF domain is a domain of CD80.
 28. An immunomodulatory protein, comprising at least one affinity modified CD80 immunoglobulin superfamily (IgSF) domain comprising one or more amino acid substitution(s) in a wild-type CD80 IgSF domain, wherein the at least one affinity modified CD80 IgSF domain has increased binding to at least two cognate binding partners compared to the wild-type CD80 IgSF domain.
 29. The immunomodulatory protein of claim 27 or claim 28, wherein the cognate binding partners are CD28 and PD-L1.
 30. The immunomodulatory protein of any of claims 27-29, wherein the wild-type IgSF domain is an IgV domain and/or the affinity modified CD80 domain is an affinity modified IgV domain.
 31. The immunomodulatory protein of any of claims 27-30, wherein the affinity-modified domain comprises at least 85% sequence identity to a wild-type CD80 domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in SEQ ID NO:1.
 32. The immunomodulatory protein of any of claims 1-31, wherein the at least one affinity modified IgSF domain comprises at least 1 and no more than twenty amino acid substitutions in the wild-type IgSF domain.
 33. The immunomodulatory protein of any of claims 1-32, wherein the at least one affinity modified IgSF domain comprises at least 1 and no more than ten amino acid substitutions in the wild-type IgSF domain.
 34. The immunomodulatory protein of any of claims 1-33, wherein the at least one affinity modified IgSF domain comprises at least 1 and no more than five amino acid substitutions in the wild-type IgSF domain.
 35. The immunomodulatory protein of any of claims 1-34, wherein the affinity modified IgSF domain has at least 120% of the binding affinity as its wild-type IgSF domain to each of the at least two cognate binding partners.
 36. The immunomodulatory protein of any of claims 1-35, further comprising a non-affinity modified IgSF domain.
 37. The immunomodulatory protein of any of claims 1-36, wherein the immunomodulatory protein is soluble.
 38. The immunomodulatory protein of any of claims 1-37, wherein the immunomodulatory protein lacks a transmembrane domain or a cytoplasmic domain.
 39. The immunomodulatory protein of any of claims 1-38, comprising only the extracellular domain (ECD) or a specific binding fragment thereof comprising the affinity modified IgSF domain.
 40. The immunomodulatory protein of any of claims 1-39, wherein the immunomodulatory protein is glycosylated or pegylated.
 41. The immunomodulatory protein of any of claims 1-40 that is linked to a multimerization domain.
 42. The immunomodulatory protein of any of claims 1-41 that is linked to an Fc domain or a variant thereof with reduced effector function.
 43. The immunomodulatory protein of claim 42, wherein the Fc domain is an IgG domain, an IgG2 domain or is a variant thereof with reduced effector function.
 44. The immunomodulatory protein of any of claims 39-41, wherein: the Fc domain is mammalian, optionally human; or the variant Fc domain comprises one or more amino acid modifications compared to an unmodified Fc domain that is mammalian, optionally human.
 45. The immunomodulatory protein of any one of claims 42-44, wherein the Fc domain or variant thereof comprises the sequence of amino acids set forth in SEQ ID NO:226 or SEQ ID NO:227 or a sequence of amino acids that exhibits at least 85% sequence identity to SEQ ID NO:226 or SEQ ID NO:227.
 46. The immunomodulatory protein of any of claims 38-41, wherein the immunomodulatory protein is linked indirectly via a linker.
 47. The immunomodulatory protein of any of claims 41-46 that is a dimer.
 48. The immunomodulatory protein of any of claim 1-47, wherein the immunomodulatory protein is attached to a liposomal membrane.
 49. An immunomodulatory protein, comprising at least two non-immunoglobulin immunoglobulin superfamily (IgSF) domains, wherein: at least one of the non-immunoglobulin modified IgSF domain is affinity-modified to exhibit altered binding to its cognate binding partner; and the at least two non-immunoglobulin modified IgSF domain each independently specifically bind to at least one different cognate binding partner.
 50. The immunomodulatory protein of claim 49, wherein the each of the at least two non-immunoglobulin IgSF domains are affinity-modified IgSF domains, wherein the first non-immunoglobulin modified IgSF domain comprises one or more amino acid substitutions in a first wild-type-type IgSF domain and the second non-immunoglobulin modified IgSF domain comprises one or more amino acid substitutions in a second wild-type IgSF domain.
 51. The immunomodulatory protein of claim 50, wherein: the first non-immunoglobulin modified IgSF domain exhibits altered binding to at least one of its cognate binding partner(s) compared to the first wild-type IgSF domain; and the second non-immunoglobulin modified IgSF domain exhibits altered binding to at least one of its cognate binding partner(s) compared to the second wild-type IgSF domain.
 52. The immunomodulatory protein of any one of claims 49-51, wherein the different cognate binding partners are cell surface molecular species expressed on the surface of a mammalian cell.
 53. The immunomodulatory protein of claim 52, wherein the different cell surface molecular species are expressed in cis configuration or trans configuration.
 54. The immunomodulatory protein of claim 52 or claim 53, wherein the mammalian cell is one of two mammalian cells forming an immunological synapse (IS) and the different cell surface molecular species is expressed on at least one of the two mammalian cells forming the IS.
 55. The immunomodulatory protein of any of claims 52-54, wherein at least one of the mammalian cells is a lymphocyte.
 56. The immunomodulatory protein of claim 55, wherein the lymphocyte is an NK cell or a T cell.
 57. The immunomodulatory protein of claim 55 or claim 56, wherein binding of the immunomodulatory protein to the cell modulates the immunological activity of the lymphocyte.
 58. The immunomodulatory protein of claim 57, wherein the immunomodulatory protein is capable of effecting increased immunological activity compared to the wild-type protein comprising the wild-type IgSF domain.
 59. The immunomodulatory protein of claim 57, wherein the immunomodulatory protein is capable of effecting decreased immunological activity compared to the wild-type protein comprising the wild-type IgSF domain.
 60. The immunomodulatory protein of any of claims 52-59, wherein at least one of the mammalian cells is a tumor cell.
 61. The immunomodulatory protein of any of claims 52-60, wherein the mammalian cells are human cells.
 62. The immunomodulatory protein of any of claims 54-61, wherein the immunomodulatory protein is capable of specifically binding to the two mammalian cells forming the IS.
 63. The immunomodulatory protein of any of claims 49-62, wherein the first and second modified IgSF domains each comprise one or more amino acid substitutions in different wild-type IgSF domains.
 64. The immunomodulatory protein of claim 63, wherein the different wild-type IgSF domains are from different IgSF family members.
 65. The immunomodulatory protein of any of claims 49-64, wherein the first and second modified IgSF domains are non-wild-type combinations.
 66. The immunomodulatory protein of any of claims 49-65, wherein the first wild-type IgSF domain and second wild-type IgSF domain each individually is from an IgSF family member of a family selected from Signal-Regulatory Protein (SIRP) Family, Triggering Receptor Expressed On Myeloid Cells Like (TREML) Family, Carcinoembryonic Antigen-related Cell Adhesion Molecule (CEACAM) Family, Sialic Acid Binding Ig-Like Lectin (SIGLEC) Family, Butyrophilin Family, B7 family, CD28 family, V-set and Immunoglobulin Domain Containing (VSIG) family, V-set transmembrane Domain (VSTM) family, Major Histocompatibility Complex (MHC) family, Signaling lymphocytic activation molecule (SLAM) family, Leukocyte immunoglobulin-like receptor (LIR), Nectin (Nec) family, Nectin-like (NECL) family, Poliovirus receptor related (PVR) family, Natural cytotoxicity triggering receptor (NCR) family, T cell immunoglobulin and mucin (TIM) family or Killer-cell immunoglobulin-like receptors (KIR) family.
 67. The immunomodulatory protein of any of claims 49-66, wherein the first wild-type IgSF domain and second wild-type IgSF domain each individually is from an IgSF member selected from CD80, CD86, PD-L1, PD-L2, ICOS Ligand, B7-H3, B7-H4, CD28, CTLA4, PD-1, ICOS, BTLA, CD4, CD8-alpha, CD8-beta, LAG3, TIM-3, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, CD200R or Nkp30.
 68. The immunomodulatory protein of any of claims 49-67, wherein the first modified IgSF domain and the second modified IgSF domain each individually comprises at least 85% sequence identity to a wild-type IgSF domain or a specific binding fragment thereof contained in the sequence of amino acids set forth in any of SEQ ID NOS: 1-27.
 69. The immunomodulatory protein of any of claims 49-68, wherein the first and second wild-type IgSF domain each individually is a member of the B7 family.
 70. The immunomodulatory protein of claim 69, wherein the first and second wild-type IgSF domain each individually is from CD80, CD86 or ICOSLG.
 71. The immunomodulatory protein of any of claims 49-68, wherein the first or second wild-type IgSF domain is from a member of the B7 family and the other of the first or second wild-type IgSF domain is from another IgSF family.
 72. The immunomodulatory protein of any of claims 49-68 and 71, wherein the first and second wild-type IgSF domain is from ICOSLG and NKp30.
 73. The immunomodulatory protein of any of claims 49-68 and 71, wherein the first and second wild-type IgSF domain is from CD80 and NKp30.
 74. The immunomodulatory protein of any of claims 49-73, wherein the first and second wild-type IgSF domain each individually is a human IgSF member.
 75. The immunomodulatory protein of any of claims 49-74, wherein the first and second wild-type IgSF domain each individually is an IgV domain, and IgC1 domain, an IgC2 domain or a specific binding thereof.
 76. The immunomodulatory protein of any of claims 49-75, wherein the first non-immunoglobulin modified domain and the second non-immunoglobulin modified domain each individually is a modified IgV domain, modified IgC1 domain or a modified IgC2 domain or is a specific binding fragment thereof comprising the one or more amino acid substitutions.
 77. The immunomodulatory protein of any of claims 49-76, wherein at least one of the first non-immunoglobulin modified domain or the second non-immunoglobulin modified domain is a modified IgV domain.
 78. The immunomodulatory protein of any of claims 49-77, wherein the first non-immunoglobulin modified IgSF domain and the second non-immunoglobulin modified IgSF domain each individually comprise 1 and no more than twenty amino acid substitutions.
 79. The immunomodulatory protein of any of claims 49-78, wherein the first non-immunoglobulin modified IgSF domain and the second non-immunoglobulin modified IgSF domain each individually comprise 1 and no more than ten amino acid substitutions.
 80. The immunomodulatory protein of any of claims 49-79, wherein the first non-immunoglobulin modified IgSF domain and the second non-immunoglobulin modified IgSF domain each individually comprise 1 and no more than five amino acid substitutions.
 81. The immunomodulatory protein of any of claims 49-80, wherein at least one of the first or second non-immunoglobulin modified IgSF domain has between 10% and 90% of the binding affinity of the wild-type IgSF domain to at least one of its cognate binding partner.
 82. The immunomodulatory protein of any of claims 49-81, wherein at least one of the first of second non-immunoglobulin modified IgSF domain has at least 120% of the binding affinity of the wild-type IgSF domain to at least one of its cognate binding partner.
 83. The immunomodulatory protein of any of claims 49-80 and 82, wherein the first and second non-immunoglobulin modified IgSF domain each individually has at least 120% of the binding affinity of the wild-type IgSF domain to at least one of its cognate binding partner.
 84. The immunomodulatory protein of any of claims 49-83, wherein the immunomodulatory protein is soluble.
 85. The immunomodulatory protein of any of claims 49-84, wherein the immunomodulatory protein is glycosylated or pegylated.
 86. The immunomodulatory protein of any of claims 49-85 that is linked to a multimerization domain.
 87. The immunomodulatory protein of any of claims 49-86 that is linked to an Fc domain or a variant thereof with reduced effector function.
 88. The immunomodulatory protein of claim 87, wherein the Fc domain is an IgG domain, an IgG2 domain or is a variant thereof with reduced effector function.
 89. The immunomodulatory protein of claim 87 or claim 88, wherein: the Fc domain is mammalian, optionally human; or the variant Fc domain comprises one or more amino acid modifications compared to an unmodified Fc domain that is mammalian, optionally human.
 90. The immunomodulatory protein of any one of claims 87-89, wherein the Fc domain or variant thereof comprises the sequence of amino acids set forth in SEQ ID NO:226 or SEQ ID NO:227 or a sequence of amino acids that exhibits at least 85% sequence identity to SEQ ID NO:226 or SEQ ID NO:227.
 91. The immunomodulatory protein of any of claims 86-90, wherein the variant CD80 polypeptide is linked indirectly via a linker.
 92. The immunomodulatory protein of any of claims 86-91 that is a dimer.
 93. The immunomodulatory protein of any of claims 49-92, further comprising one or more additional non-immunoglobulin IgSF domain that is the same of different from the first or second non-immunoglobulin modified IgSF domain.
 94. The immunomodulatory protein of claim 93, wherein the one or more additional non-immunoglobulin IgSF domain is an affinity modified IgSF domain.
 95. The immunomodulatory protein of any of claim 49-94, wherein the immunomodulatory protein is attached to a liposomal membrane.
 96. A nucleic acid molecule, encoding the immunomodulatory polypeptide of any of claims 1-95.
 97. The nucleic acid molecule of claim 96 that is synthetic nucleic acid.
 98. The nucleic acid molecule of claim 96 or claim 97 that is cDNA.
 99. A vector, comprising the nucleic acid molecule of any of claims 96-98.
 100. The vector of claim 99 that is an expression vector.
 101. A cell, comprising the vector of claim 99 or claim
 100. 102. The cell of claim 101 that is a eukaryotic cell or prokaryotic cell.
 103. A method of producing an immunomodulatory protein, comprising introducing the nucleic acid molecule of any of claims 96-98 or vector of claim 99 or claim 100 into a host cell under conditions to express the protein in the cell.
 104. The method of claim 103, further comprising isolating or purifying the immunomodulatory protein from the cell.
 105. A pharmaceutical composition, comprising the immunomodulatory protein of any of claims 1-95.
 106. The pharmaceutical composition of claim 105, comprising a pharmaceutically acceptable excipient.
 107. The pharmaceutical composition of claim 105 or claim 106 that is sterile.
 108. An article of manufacture comprising the pharmaceutical composition of any of claims 105-107 in a vial.
 109. The article of manufacture of claim 108, wherein the vial is sealed.
 110. A kit comprising the pharmaceutical composition of any of claims 105-107, and instructions for use.
 111. A kit comprising the article of manufacture according to claim 108 or claim 109, and instructions for use.
 112. A method of modulating an immune response in a subject, comprising administering therapeutically effective amount of the immunomodulatory protein of any of claims 1-95 to the subject.
 113. The method of claim 112, wherein modulating the immune response treats a disease or condition in the subject.
 114. The method of claim 112 or claim 113, wherein the immune response is increased.
 115. The method of claim 114, wherein the disease or condition is a tumor or cancer.
 116. The method of claim 114 or claim 115, wherein the disease or condition is selected from melanoma, lung cancer, bladder cancer or a hematological malignancy.
 117. The method of claim 112 or claim 113, wherein the immune response is decreased.
 118. The method of claim 117, wherein the disease or condition is an inflammatory disease or condition.
 119. The method of claim 117 or claim 118, wherein the disease or condition is selected from Crohn's disease, ulcerative colitis, multiple sclerosis, asthma, rheumatoid arthritis, or psoriasis.
 120. A method of identifying an affinity modified immunomodulatory protein, comprising: a) contacting a modified protein comprising at least one non-immunoglobulin modified immunoglobulin superfamily (IgSF) domain or specific binding fragment thereof with at least two cognate binding partners under conditions capable of effecting binding of the protein with the at least two cognate binding partners, wherein the at least one modified IgSF domain comprises one or more amino acid substitutions in a wild-type IgSF domain; b) identifying a modified protein comprising the modified IgSF domain that has increased binding to at least one of the two cognate binding partners compared to a protein comprising the wild-type IgSF domain; and c) selecting a modified protein comprising the modified IgSF domain that binds non-competitively to the at least two cognate binding partners, thereby identifying the affinity modified immunomodulatory protein.
 121. The method of claim 120, wherein step b) comprises identifying a modified protein comprising a modified IgSF domain that has increased binding to each of the at least two cognate binding partners compared to a protein comprising the wild-type domain.
 122. The method of claim 120 or claim 121, wherein prior to step a), introducing one or more amino acid substitutions into the wild-type IgSF domain, thereby generating a modified protein comprising the modified IgSF domain.
 123. The method of any of claims 120-122, wherein the modified protein comprises at least two modified IgSF domains or specific binding fragments thereof, wherein the first IgSF domain comprises one or more amino acid substitutions in a first wild-type-type IgSF domain and the second non-immunoglobulin affinity modified IgSF domain comprises one or more amino acid substitutions in a second wild-type IgSF domain.
 124. The method of claim 123, wherein the first and second non-immunoglobulin affinity modified IgSF domain each specifically bind to at least one different cognate binding partner.
 125. The method of any of claims 120-124, wherein prior to selecting the modified protein, the method further comprises combining two or more modified IgSF domains or specific binding fragments thereof identified in step (b) to generate a protein containing two or more different modified IgSF domains.
 126. The method of any of claims 120-125, wherein the affinity modified protein is capable or binding the two cognate binding partners simultaneously at the same time.
 127. The method of any of claims 120-126, wherein the at least two cognate binding partners are cell surface molecular species expressed on the surface of a mammalian cell.
 128. The method of claim 127, wherein the cell surface molecular species are expressed in cis configuration or trans configuration.
 129. The method of claim 127 or claim 128, wherein the mammalian cell is one of two mammalian cells forming an immunological synapse (IS) and each of the cell surface molecular species is expressed on at least one of the two mammalian cells forming the IS.
 130. The method of any of claims 127-129, wherein at least one of the mammalian cells is a lymphocyte.
 131. The method of any of claims 127-130, wherein the lymphocyte is an NK cell or a T cell.
 132. The method of any of claims 127-131, wherein at least one of the mammalian cells is a tumor cell.
 133. The method of any of claims 127-132, wherein at least one of the mammalian cells is an antigen-presenting cell.
 134. The method of any of claims 127-133, wherein the two or more cognate binding partners are independently a ligand of an IgSF member selected from CD80, CD86, PD-L1, PD-L2, ICOS Ligand, B7-H3, B7-H4, CD28, CTLA4, PD-1, ICOS, BTLA, CD4, CD8-alpha, CD8-beta, LAG3, TIM-3, CEACAM1, TIGIT, PVR, PVRL2, CD226, CD2, CD160, CD200, CD200R or Nkp30.
 135. The method of any of claims 127-134, wherein the two or more cognate binding partners are independently a ligand of a B7 family member.
 136. The method of any of claims 127-135, wherein the two or more cognate binding partners are selected from two or more of CD28, CTLA-4, ICOS or PD-L1. 